The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. Gene Ontology The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology gene_ontology 1.2 2023-06-11 2023-08-18 https://github.com/oborel/obo-relations/ editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external term_tracker_item true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. PERSON:Alan Ruttenberg first order logic expression OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] ambiguous for taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon defined by inverse An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. annotation property cardinality A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. dispositional interpretation 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) has no connections with inherited annotation property Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) curator guidance link brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in always present in taxon This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. temporal logical macro assertion on a class measurement property has unit has start time value has end time value Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. start, days post fertilization Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. end, days post fertilization Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. start, years post birth Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 end, years post birth Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. start, months post birth Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 end, months post birth Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. month of gestation A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process has developmental stage marker Count of number of days intervening between the start of the stage and the time of coitum. For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) start, days post coitum Count of number of days intervening between the end of the stage and the time of coitum. end, days post coitum start, weeks post birth end, weeks post birth If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p is asymmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p is symmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process is relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y is indirect form of logical macro assertion on an axiom If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. is relational form of a class A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" is approximately equivalent to 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is indistinguishable from evidential logical macro assertion on an axiom A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom has evidence A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom contradicted by evidence In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. nominally disjoint with Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" 2018-03-13T23:59:29Z is directional form of 2018-03-14T00:03:16Z is positive form of 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for 2020-09-22T11:05:29Z valid_for_go_annotation_extension 2020-09-22T11:05:18Z valid_for_go_gp2term 2020-09-22T11:04:12Z valid_for_go_ontology 2020-09-22T11:05:45Z valid_for_gocam Rhea list of ChEBI terms representing the major species at pH 7.3. Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary Drosophila GO slim FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim synapse GO slim Yeast GO slim GO subset for prokaryotes label approved by the SynGO project Systematic synonym eco subset subset_property synonym_type_property consider has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has_obo_format_version has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has_scope has_synonym_type in_subset shorthand is defined by is defined by This is an experimental annotation is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by true preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external preceded_by preceded_by preceded by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external precedes precedes precedes precedes inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external bearer_of bearer_of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external participates_in participates_in participates in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). obsolete in neural circuit with true OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). obsolete upstream in neural circuit with true OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). obsolete downstream in neural circuit with true contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): contained_in obsolete contained in true contains obsolete contains true located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y cell expresses 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. 2017-07-19T17:30:36Z has ligand 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 external immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately preceded by David Osumi-Sutherland starts before David Osumi-Sutherland io RO:0002091 external starts_during starts_during X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during starts during David Osumi-Sutherland d during RO:0002092 external happens_during happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during happens during https://wiki.geneontology.org/Happens_during David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external overlaps overlaps overlaps overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external has_component has_component has component has component definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. gene product of every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y has gene product 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process expressed in c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in RO:0002216 external capable_of_part_of capable_of_part_of capable of part of capable of part of OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role agent in Obsoleted as the inverse property was obsoleted. obsolete actively participates in true OBSOLETE x has participant y if and only if x realizes some active role that inheres in y has agent obsolete has active participant true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes RO:0002233 external has_input has_input has input has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces RO:0002234 external has_output has_output has output has output https://wiki.geneontology.org/Has_output g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. over-expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. under-expressed in c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) has chemical role x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. ubiquitously expressed in y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses inverse of ubiquiotously expressed in ubiquitously expresses q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] colocalizes with ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to https://wiki.geneontology.org/Contributes_to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of (process to entity) RO:0002332 external regulates_levels_of regulates_levels_of regulates levels of regulates levels of inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect input true translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. directly produces obsolete has direct output true Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit obsolete has indirect output true This term was obsoleted because it has the same meaning as 'directly positively regulates'. obsolete directly activates true p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates This term was obsoleted because it has the same meaning as 'directly negatively regulates'. obsolete directly inhibits true p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later ubiquitinates p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities A relation that holds between two entities that have the property of being sequences or having sequences. http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. sequentially related to Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y http://www.ncbi.nlm.nih.gov/pubmed/20226267 sequentially adjacent to inverse of has start sequence starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 is start sequence of inverse of has end sequence ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 is end sequence of inverse of bounds sequence of is bound by sequence of inverse of has subsequence contained by is subsequence of x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. overlaps sequence of x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. disconnected from does not overlap sequence of inverse of downstream of sequence of is upstream of sequence of x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. is downstream of sequence of A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y is immediately downstream of sequence of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of is immediately upstream of sequence of The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) RO:0002578 external directly_regulates directly_regulates directly regulates pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating pazopanib -> pathological angiogenesis Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. treats The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. capable of inhibiting or preventing pathological process treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship benzene -> cancer [CHEBI] Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. causes disease capable of upregulating or causing pathological process c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI is marker for A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to true A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) RO:0002629 external directly_positively_regulates directly_positively_regulates directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) RO:0002630 external directly_negatively_regulates directly_negatively_regulates directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. represses expression of Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. increases expression of A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. correlated with condition p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. [072-ISO] g-depends on generically depends on The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. indirectly regulates activity of The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. indirectly activates indirectly positively regulates activity of The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. indirectly inhibits indirectly negatively regulates activity of a relation between a process and a continuant, in which the process is regulated by the small molecule continuant 2020-04-22T20:27:26Z has small molecule regulator a relation between a process and a continuant, in which the process is activated by the small molecule continuant 2020-04-22T20:28:37Z has small molecule activator a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant 2020-04-22T20:28:54Z has small molecule inhibitor p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z indirectly regulates A relation between entities in which one increases or decreases as the other does the same. directly correlated with positively correlated with A relation between entities in which one increases as the other decreases. inversely correlated with negatively correlated with A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input myristoylates inverse of myristoylates myristoylated by mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor is agonist of pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level is inverse agonist of tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level is antagonist of has_domain acetylates deacetylates methylates demethylates deubiquitinates dephosphorylates has subunit subunit of 0 100 Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. PMID:24138933 Wikipedia:Infant_mortality An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant spatial region p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity immaterial entity A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 MESH:D011984 WBbt:0005759 sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. MESH:D009474 http://en.wikipedia.org/wiki/Neuron A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 An environmental system which can sustain and allow the growth of an ecological population. EcoLexicon:habitat LTER:238 SWEETRealm:Habitat https://en.wikipedia.org/wiki/Habitat A habitat's specificity to an ecological population differentiates it from other environment classes. habitat An environmental system which can sustain and allow the growth of an ecological population. EnvO:EnvO A protein complex that possesses histone deacetylase activity. HDAC complex cellular_component GO:0000118 Note that this term represents a location, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone deacetylase activity ; GO:0004407'. histone deacetylase complex GO:0000118 A protein complex that possesses histone deacetylase activity. GOC:mah A protein complex that possesses histone acetyltransferase activity. https://github.com/geneontology/go-ontology/issues/23892 histone acetylase complex cellular_component GO:0000123 Note that this term represents a protein complex, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone acetyltransferase activity ; GO:0004402'. histone acetyltransferase complex GO:0000123 A protein complex that possesses histone acetyltransferase activity. GOC:mah true A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions. cellular_component GO:0000127 transcription factor TFIIIC complex GO:0000127 A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions. GOC:mah GOC:vw PMID:11433012 PMID:16751097 A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex. cellular_component GO:0000151 ubiquitin ligase complex GO:0000151 A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex. GOC:jh2 PMID:9529603 A ubiquitin ligase complex found in the nucleus. cellular_component GO:0000152 nuclear ubiquitin ligase complex GO:0000152 A ubiquitin ligase complex found in the nucleus. GOC:mah Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. molecular_function GO:0000166 nucleotide binding GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GOC:mah ISBN:0198547684 The formation of heterochromatin at ribosomal DNA, characterized by the modified histone H3K9me3. https://github.com/geneontology/go-ontology/issues/19238 https://github.com/geneontology/go-ontology/issues/23553 chromatin silencing at ribosomal DNA heterochromatic silencing at rDNA rDNA chromatin silencing rDNA heterochromatin assembly biological_process chromatin silencing at rDNA GO:0000183 rDNA heterochromatin formation GO:0000183 The formation of heterochromatin at ribosomal DNA, characterized by the modified histone H3K9me3. PMID:10219245 rDNA chromatin silencing GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component GO:0000228 nuclear chromosome GO:0000228 A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division GO:0000280 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. CDK holoenzyme cellular_component GO:0000307 cyclin-dependent protein kinase holoenzyme complex GO:0000307 Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner. GOC:krc PMID:11602261 Cyclin-dependent protein kinase (CDK) complex found in the cytoplasm. CDK holoenzyme cellular_component GO:0000308 cytoplasmic cyclin-dependent protein kinase holoenzyme complex GO:0000308 Cyclin-dependent protein kinase (CDK) complex found in the cytoplasm. GOC:krc The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GO:0097521 SO:0000577 centromere complex chromosome, centric region cellular_component centromere chromosome, pericentric region GO:0000775 Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. chromosome, centromeric region GO:0000775 The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GOC:cjm GOC:elh GOC:kmv GOC:pr The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GO:0000780 condensed chromosome, centric region condensed nuclear chromosome, centromeric region cellular_component condensed chromosome, centromere condensed chromosome, pericentric region GO:0000779 Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. condensed chromosome, centromeric region GO:0000779 The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome. GOC:elh GOC:kmv The end of a linear chromosome, required for the integrity and maintenance of the end. A chromosome telomere usually includes a region of telomerase-encoded repeats the length of which rarely exceeds 20 bp each and that permits the formation of a telomeric loop (T-loop). The telomeric repeat region is usually preceded by a sub-telomeric region that is gene-poor but rich in repetitive elements. Some telomeres only consist of the latter part (for eg. D. melanogaster telomeres). GO:0000784 SO:0000624 nuclear chromosome, telomere nuclear chromosome, telomeric region cellular_component telomere GO:0000781 Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. chromosome, telomeric region GO:0000781 The end of a linear chromosome, required for the integrity and maintenance of the end. A chromosome telomere usually includes a region of telomerase-encoded repeats the length of which rarely exceeds 20 bp each and that permits the formation of a telomeric loop (T-loop). The telomeric repeat region is usually preceded by a sub-telomeric region that is gene-poor but rich in repetitive elements. Some telomeres only consist of the latter part (for eg. D. melanogaster telomeres). GOC:elh A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome. cellular_component GO:0000782 Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. telomere cap complex GO:0000782 A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome. GOC:elh A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome. cellular_component GO:0000783 Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. nuclear telomere cap complex GO:0000783 A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome. GOC:elh The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GO:0000789 GO:0000790 GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin cellular_component chromosome scaffold GO:0000785 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromatin GO:0000785 The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GOC:elh PMID:20404130 A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 GO:0005719 GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin cellular_component nuclear euchromatin GO:0000791 euchromatin GO:0000791 A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. PMID:32017156 A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 GO:0005720 GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin transcriptionally silent chromatin nuclear heterochromatin cellular_component GO:0000792 heterochromatin GO:0000792 A compact and highly condensed form of chromatin that is refractory to transcription. PMID:32017156 A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. cellular_component cytoplasmic mitotic chromosome metaphase chromosome mitotic chromosome GO:0000793 Note that this term can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes an 'open mitosis' in which the nuclear envelope breaks down during mitosis. condensed chromosome GO:0000793 A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. GOC:elh A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome. cellular_component meiotic chromosome nuclear mitotic chromosome GO:0000794 Note that this term and its children can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes a 'closed mitosis' in which the nuclear envelope does not break down during mitosis and for gene products that localize to a meiotic chromosome. condensed nuclear chromosome GO:0000794 A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome. GOC:elh true A multisubunit complex that is located at the replication origins of a chromosome. Wikipedia:Origin_recognition_complex ORC origin of replication recognition complex cellular_component GO:0000808 origin recognition complex GO:0000808 A multisubunit complex that is located at the replication origins of a chromosome. GOC:elh A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits. SWR-C cellular_component GO:0000812 Swr1 complex GO:0000812 A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits. GOC:rb PMID:14645854 PMID:14690608 PMID:19355820 The nucleus of a male germ cell, a reproductive cell in males. GO:0043081 male germ-cell nucleus cellular_component GO:0001673 male germ cell nucleus GO:0001673 The nucleus of a male germ cell, a reproductive cell in males. CL:0000015 GOC:hjd GOC:mtg_sensu The nucleus of the female germ cell, a reproductive cell in females. GO:0043080 female germ-cell nucleus cellular_component GO:0001674 female germ cell nucleus GO:0001674 The nucleus of the female germ cell, a reproductive cell in females. CL:0000021 GOC:hjd The pronucleus originating from the ovum that is being fertilized. cellular_component GO:0001939 female pronucleus GO:0001939 The pronucleus originating from the ovum that is being fertilized. GOC:hjd ISBN:0198506732 The pronucleus originating from the spermatozoa that was involved in fertilization. cellular_component GO:0001940 male pronucleus GO:0001940 The pronucleus originating from the spermatozoa that was involved in fertilization. GOC:hjd ISBN:0198506732 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function GO:0003674 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt Binding to a nucleic acid. GO:0000496 base pairing molecular_function GO:0003676 nucleic acid binding GO:0003676 Binding to a nucleic acid. GOC:jl Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0043566 plasmid binding molecular_function microtubule/chromatin interaction structure specific DNA binding structure-specific DNA binding GO:0003677 DNA binding GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb GOC:vw Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. lamin/chromatin binding microtubule/chromatin interaction nuclear membrane vesicle binding to chromatin molecular_function GO:0003682 chromatin binding GO:0003682 Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. GOC:jl ISBN:0198506732 PMID:20404130 A transcription regulator activity that modulates the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. https://github.com/geneontology/go-ontology/issues/15536 https://github.com/geneontology/go-ontology/issues/15665 https://github.com/geneontology/go-ontology/issues/15998 https://github.com/geneontology/go-ontology/issues/20253 https://github.com/geneontology/go-ontology/issues/20464 https://github.com/geneontology/go-ontology/issues/20862 https://github.com/geneontology/go-ontology/issues/20962 krc 2010-11-24T03:02:15Z GO:0001104 GO:0016455 transcription cofactor activity transcriptional co-regulator molecular_function RNA polymerase II transcriptional cofactor activity GO:0003712 Usage guidance: Most transcription coregulators do not bind DNA. Those that do usually bind DNA either in a non-specific or non-direct manner. If a protein binds DNA specifically, consider annotating to GO:0003700 DNA binding transcription factor activity. transcription coregulator activity GO:0003712 A transcription regulator activity that modulates the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coregulators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. GOC:txnOH-2018 PMID:10213677 PMID:16858867 PMID:24203923 PMID:25957681 Wikipedia:Transcription_coregulator A transcription coregulator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coactivators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator. https://github.com/geneontology/go-ontology/issues/15665 https://github.com/geneontology/go-ontology/issues/15998 https://github.com/geneontology/go-ontology/issues/20253 https://github.com/geneontology/go-ontology/issues/20464 krc 2010-11-24T03:08:19Z GO:0001105 transcription co-activator activity molecular_function RNA polymerase II transcription co-activator activity RNA polymerase II transcription coactivator activity RNA polymerase II transcription mediator activity GO:0003713 For usage guidance, see comment in GO:0003712 ; transcription coregulator activity. transcription coactivator activity GO:0003713 A transcription coregulator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound DNA-binding transcription factor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coactivators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator. GOC:txnOH-2018 PMID:10213677 PMID:16858867 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine. GO:0008326 DNA cytosine methylase activity DNA-cytosine methyltransferase activity cytosine DNA methylase activity cytosine DNA methyltransferase activity deoxyribonucleic methylase activity EC:2.1.1.37 MetaCyc:2.1.1.73-RXN RHEA:13681 site-specific DNA-methyltransferase (cytosine-specific) activity molecular_function DNA 5-cytosine methylase activity DNA cytosine C(5) methylase activity DNA cytosine C5 methylase activity DNA-cytosine 5-methylase activity S-adenosyl-L-methionine:DNA (cytosine-5-)-methyltransferase activity cytosine 5-methyltransferase activity cytosine-specific DNA methyltransferase activity deoxyribonucleic (cytosine-5-)-methyltransferase activity deoxyribonucleic acid (cytosine-5-)-methyltransferase activity methylphosphotriester-DNA methyltransferase activity modification methylase activity restriction-modification system activity type II DNA methylase activity GO:0003886 Note that EC:2.1.1.73 was deleted from EC as the reaction is performed by DNA (cytosine-5-)-methyltransferase (EC:2.1.1.37). DNA (cytosine-5-)-methyltransferase activity GO:0003886 Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine. EC:2.1.1.37 DNA cytosine methylase activity EC:2.1.1.37 DNA-cytosine methyltransferase activity EC:2.1.1.37 cytosine DNA methylase activity EC:2.1.1.37 cytosine DNA methyltransferase activity EC:2.1.1.37 deoxyribonucleic methylase activity EC:2.1.1.37 site-specific DNA-methyltransferase (cytosine-specific) activity EC:2.1.1.37 DNA 5-cytosine methylase activity EC:2.1.1.37 DNA cytosine C(5) methylase activity EC:2.1.1.37 DNA cytosine C5 methylase activity EC:2.1.1.37 DNA-cytosine 5-methylase activity EC:2.1.1.37 S-adenosyl-L-methionine:DNA (cytosine-5-)-methyltransferase activity EC:2.1.1.37 cytosine 5-methyltransferase activity EC:2.1.1.37 cytosine-specific DNA methyltransferase activity EC:2.1.1.37 deoxyribonucleic (cytosine-5-)-methyltransferase activity EC:2.1.1.37 deoxyribonucleic acid (cytosine-5-)-methyltransferase activity EC:2.1.1.37 methylphosphotriester-DNA methyltransferase activity EC:2.1.1.37 modification methylase activity EC:2.1.1.37 restriction-modification system activity EC:2.1.1.37 type II DNA methylase activity EC:2.1.1.37 Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone. GO:0004403 GO:0004404 GO:0004405 GO:0004406 GO:0043166 GO:0046971 EC:2.3.1.48 MetaCyc:HISTONE-ACETYLTRANSFERASE-RXN RHEA:21992 Reactome:R-HSA-3301237 Reactome:R-HSA-3301345 Reactome:R-HSA-3318413 Reactome:R-HSA-3318415 Reactome:R-HSA-3318486 Reactome:R-HSA-3321805 Reactome:R-HSA-3321883 Reactome:R-HSA-3321975 Reactome:R-HSA-3451147 Reactome:R-HSA-3662318 Reactome:R-HSA-3662335 Reactome:R-HSA-3697008 Reactome:R-HSA-3697920 Reactome:R-HSA-5144542 Reactome:R-HSA-5250938 histone acetylase activity histone lysine acetyltransferase activity H2A/H2B histone acetyltransferase activity H3/H4 histone acetyltransferase activity H4/H2 histone acetyltransferase activity H4/H2A acetyltransferase activity molecular_function acetyl-CoA:histone acetyltransferase activity histone acetokinase activity histone transacetylase activity nucleosome-histone acetyltransferase activity GO:0004402 histone acetyltransferase activity GO:0004402 Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone. EC:2.3.1.48 Reactome:R-HSA-3301237 KAT2 complexes acetylate histone H3 Reactome:R-HSA-3301345 Elongator complex acetylates replicative histone H3, H4 Reactome:R-HSA-3318413 KAT7-containing ING4/5 complexes acetylate Me3K-histone H3 Reactome:R-HSA-3318415 ATF2 acetylates histone H2B, H4 Reactome:R-HSA-3318486 KAT6A, KAT6B-containing ING5 complexes acetylate replicative histone H3 Reactome:R-HSA-3321805 NSL acetylates histone H4 Reactome:R-HSA-3321883 MSL acetylates histone H4 Reactome:R-HSA-3321975 NuA4 complex acetylates histone H2A, HIST1H4 Reactome:R-HSA-3451147 KAT5 HAT complex acetylates TCF4 gene at histone H4 Reactome:R-HSA-3662318 Type B histone acetlytransferase complex acetylates histone H4 Reactome:R-HSA-3662335 EP300 acetylates histone H2A, H2B, H3, H4 Reactome:R-HSA-3697008 CREBBP acetylates histone H2B, H3, H4 Reactome:R-HSA-3697920 CLOCK acetylates lysine-10 of histone H3, H4 Reactome:R-HSA-5144542 CLOCK acetylates lysine-15 of histone H3, H4 Reactome:R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9 acetyl-CoA:histone acetyltransferase activity EC:2.3.1.48 histone acetokinase activity EC:2.3.1.48 histone transacetylase activity EC:2.3.1.48 nucleosome-histone acetyltransferase activity EC:2.3.1.48 Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes. https://github.com/geneontology/go-ontology/issues/22295 EC:3.5.1.98 MetaCyc:3.5.1.98-RXN RHEA:58196 Reactome:R-HSA-2545203 Reactome:R-HSA-2545253 Reactome:R-HSA-3769447 Reactome:R-HSA-3777129 Reactome:R-HSA-3782637 Reactome:R-HSA-3782655 Reactome:R-HSA-427514 Reactome:R-HSA-433672 Reactome:R-HSA-6805650 molecular_function GO:0004407 histone deacetylase activity GO:0004407 Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes. PMID:9893272 RHEA:58196 Reactome:R-HSA-2545203 Deacetylation of cleaved cohesin Reactome:R-HSA-2545253 Deacetylation of cohesin Reactome:R-HSA-3769447 HDAC1:2-containing complex deacetylate histones Reactome:R-HSA-3777129 HDAC3 containing complexes deacetylate histone Reactome:R-HSA-3782637 HDAC8 deacetylates histones Reactome:R-HSA-3782655 HDAC10 deacetylates histone Reactome:R-HSA-427514 eNoSC deacetylates histone H3 Reactome:R-HSA-433672 NoRC:HDAC:DNMT deacetylates histone H4 and methylates histone H3 Reactome:R-HSA-6805650 MTA2-NuRD complex deacetylates TP53 Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. GO:0050222 MetaCyc:PROTEIN-KINASE-RXN Reactome:R-HSA-156832 Reactome:R-HSA-937034 Reactome:R-HSA-9604606 Reactome:R-HSA-9673284 Reactome:R-HSA-975139 protamine kinase activity molecular_function GO:0004672 Note that triphosphate is used as a phosphate donor by at least one kinase. protein kinase activity GO:0004672 Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. MetaCyc:PROTEIN-KINASE-RXN Reactome:R-HSA-156832 INF-gamma induced phosphorylation of L13a Reactome:R-HSA-937034 IRAK1 phosphorylates Pellino Reactome:R-HSA-9604606 Unknown kinase phosphorylates NICD4 Reactome:R-HSA-9673284 GTP-bound RAC1 contributes to MAPK8 activation Reactome:R-HSA-975139 IRAK1 phosphorylates Pellino upon TLR7/8 or 9 activation Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. GO:0004718 RHEA:10596 Reactome:R-HSA-112333 Reactome:R-HSA-114600 Reactome:R-HSA-1168394 Reactome:R-HSA-1169421 Reactome:R-HSA-1225952 Reactome:R-HSA-1225960 Reactome:R-HSA-1247844 Reactome:R-HSA-1248655 Reactome:R-HSA-1248694 Reactome:R-HSA-1250195 Reactome:R-HSA-1250315 Reactome:R-HSA-1250348 Reactome:R-HSA-1251922 Reactome:R-HSA-1295540 Reactome:R-HSA-1295609 Reactome:R-HSA-1307963 Reactome:R-HSA-1433418 Reactome:R-HSA-1433454 Reactome:R-HSA-1433488 Reactome:R-HSA-1433506 Reactome:R-HSA-1433542 Reactome:R-HSA-1470009 Reactome:R-HSA-1472121 Reactome:R-HSA-1524186 Reactome:R-HSA-1671691 Reactome:R-HSA-170070 Reactome:R-HSA-170156 Reactome:R-HSA-170991 Reactome:R-HSA-171011 Reactome:R-HSA-174164 Reactome:R-HSA-177930 Reactome:R-HSA-177934 Reactome:R-HSA-177937 Reactome:R-HSA-182969 Reactome:R-HSA-183058 Reactome:R-HSA-1839065 Reactome:R-HSA-1839067 Reactome:R-HSA-1839098 Reactome:R-HSA-1839110 Reactome:R-HSA-1839112 Reactome:R-HSA-186786 Reactome:R-HSA-1888198 Reactome:R-HSA-190326 Reactome:R-HSA-190385 Reactome:R-HSA-190388 Reactome:R-HSA-190408 Reactome:R-HSA-190413 Reactome:R-HSA-190427 Reactome:R-HSA-190429 Reactome:R-HSA-191062 Reactome:R-HSA-191636 Reactome:R-HSA-1963581 Reactome:R-HSA-1963582 Reactome:R-HSA-1963586 Reactome:R-HSA-1982066 Reactome:R-HSA-2012073 Reactome:R-HSA-2012082 Reactome:R-HSA-2012087 Reactome:R-HSA-201521 Reactome:R-HSA-202165 Reactome:R-HSA-202168 Reactome:R-HSA-202174 Reactome:R-HSA-202216 Reactome:R-HSA-202233 Reactome:R-HSA-202245 Reactome:R-HSA-202248 Reactome:R-HSA-202291 Reactome:R-HSA-202307 Reactome:R-HSA-2023455 Reactome:R-HSA-2023460 Reactome:R-HSA-2029268 Reactome:R-HSA-2029449 Reactome:R-HSA-2029453 Reactome:R-HSA-2029459 Reactome:R-HSA-2029984 Reactome:R-HSA-2029989 Reactome:R-HSA-2033485 Reactome:R-HSA-2033486 Reactome:R-HSA-2033488 Reactome:R-HSA-2033490 Reactome:R-HSA-2038387 Reactome:R-HSA-2038944 Reactome:R-HSA-205289 Reactome:R-HSA-210291 Reactome:R-HSA-210872 Reactome:R-HSA-212710 Reactome:R-HSA-2130194 Reactome:R-HSA-2197698 Reactome:R-HSA-2201322 Reactome:R-HSA-2395412 Reactome:R-HSA-2395439 Reactome:R-HSA-2395801 Reactome:R-HSA-2396594 Reactome:R-HSA-2404193 Reactome:R-HSA-2404199 Reactome:R-HSA-2424484 Reactome:R-HSA-2424486 Reactome:R-HSA-2424487 Reactome:R-HSA-2428926 Reactome:R-HSA-2454208 Reactome:R-HSA-2454239 Reactome:R-HSA-2586553 Reactome:R-HSA-2586555 Reactome:R-HSA-2671742 Reactome:R-HSA-2671829 Reactome:R-HSA-2671850 Reactome:R-HSA-2730833 Reactome:R-HSA-2730843 Reactome:R-HSA-2730851 Reactome:R-HSA-2730858 Reactome:R-HSA-2730860 Reactome:R-HSA-2730862 Reactome:R-HSA-2730882 Reactome:R-HSA-2730884 Reactome:R-HSA-2730886 Reactome:R-HSA-2730888 Reactome:R-HSA-3215391 Reactome:R-HSA-354073 Reactome:R-HSA-354124 Reactome:R-HSA-372693 Reactome:R-HSA-373747 Reactome:R-HSA-373750 Reactome:R-HSA-374701 Reactome:R-HSA-377640 Reactome:R-HSA-380780 Reactome:R-HSA-388831 Reactome:R-HSA-388833 Reactome:R-HSA-389083 Reactome:R-HSA-389086 Reactome:R-HSA-389159 Reactome:R-HSA-389354 Reactome:R-HSA-389762 Reactome:R-HSA-391156 Reactome:R-HSA-391865 Reactome:R-HSA-391866 Reactome:R-HSA-391871 Reactome:R-HSA-3928578 Reactome:R-HSA-3928580 Reactome:R-HSA-3928583 Reactome:R-HSA-3928594 Reactome:R-HSA-3928604 Reactome:R-HSA-3928610 Reactome:R-HSA-3928627 Reactome:R-HSA-3928648 Reactome:R-HSA-399934 Reactome:R-HSA-399946 Reactome:R-HSA-399947 Reactome:R-HSA-4093332 Reactome:R-HSA-418163 Reactome:R-HSA-418859 Reactome:R-HSA-418872 Reactome:R-HSA-419646 Reactome:R-HSA-428888 Reactome:R-HSA-429441 Reactome:R-HSA-429449 Reactome:R-HSA-432129 Reactome:R-HSA-434836 Reactome:R-HSA-4420117 Reactome:R-HSA-4420121 Reactome:R-HSA-4420128 Reactome:R-HSA-4420206 Reactome:R-HSA-443817 Reactome:R-HSA-445076 Reactome:R-HSA-445084 Reactome:R-HSA-445085 Reactome:R-HSA-445091 Reactome:R-HSA-451942 Reactome:R-HSA-452097 Reactome:R-HSA-452100 Reactome:R-HSA-452122 Reactome:R-HSA-508282 Reactome:R-HSA-5218640 Reactome:R-HSA-5218642 Reactome:R-HSA-5218806 Reactome:R-HSA-5218809 Reactome:R-HSA-5218812 Reactome:R-HSA-5218820 Reactome:R-HSA-5218828 Reactome:R-HSA-5218830 Reactome:R-HSA-5218851 Reactome:R-HSA-5357429 Reactome:R-HSA-5607745 Reactome:R-HSA-5607750 Reactome:R-HSA-5621355 Reactome:R-HSA-5621363 Reactome:R-HSA-5621370 Reactome:R-HSA-5624486 Reactome:R-HSA-5637795 Reactome:R-HSA-5637796 Reactome:R-HSA-5654147 Reactome:R-HSA-5654149 Reactome:R-HSA-5654151 Reactome:R-HSA-5654222 Reactome:R-HSA-5654397 Reactome:R-HSA-5654407 Reactome:R-HSA-5654408 Reactome:R-HSA-5654418 Reactome:R-HSA-5654428 Reactome:R-HSA-5654545 Reactome:R-HSA-5654575 Reactome:R-HSA-5654578 Reactome:R-HSA-5654582 Reactome:R-HSA-5654587 Reactome:R-HSA-5654605 Reactome:R-HSA-5654607 Reactome:R-HSA-5654628 Reactome:R-HSA-5654631 Reactome:R-HSA-5654634 Reactome:R-HSA-5654653 Reactome:R-HSA-5654655 Reactome:R-HSA-5655243 Reactome:R-HSA-5655268 Reactome:R-HSA-5655270 Reactome:R-HSA-5655278 Reactome:R-HSA-5655284 Reactome:R-HSA-5655301 Reactome:R-HSA-5655341 Reactome:R-HSA-5683930 Reactome:R-HSA-5686587 Reactome:R-HSA-5690702 Reactome:R-HSA-6784006 Reactome:R-HSA-6784319 Reactome:R-HSA-6790087 Reactome:R-HSA-6806974 Reactome:R-HSA-68954 Reactome:R-HSA-69195 Reactome:R-HSA-873918 Reactome:R-HSA-873919 Reactome:R-HSA-873922 Reactome:R-HSA-873924 Reactome:R-HSA-879907 Reactome:R-HSA-879909 Reactome:R-HSA-879925 Reactome:R-HSA-8847977 Reactome:R-HSA-8848005 Reactome:R-HSA-8848077 Reactome:R-HSA-8848124 Reactome:R-HSA-8848436 Reactome:R-HSA-8848606 Reactome:R-HSA-8848726 Reactome:R-HSA-8848758 Reactome:R-HSA-8848776 Reactome:R-HSA-8848818 Reactome:R-HSA-8848873 Reactome:R-HSA-8848975 Reactome:R-HSA-8849032 Reactome:R-HSA-8849042 Reactome:R-HSA-8849068 Reactome:R-HSA-8849102 Reactome:R-HSA-8849463 Reactome:R-HSA-8851890 Reactome:R-HSA-8851933 Reactome:R-HSA-8853309 Reactome:R-HSA-8853313 Reactome:R-HSA-8853325 Reactome:R-HSA-8855237 Reactome:R-HSA-8857555 Reactome:R-HSA-8857577 Reactome:R-HSA-8857583 Reactome:R-HSA-8857925 Reactome:R-HSA-8867041 Reactome:R-HSA-8874078 Reactome:R-HSA-8874080 Reactome:R-HSA-8874082 Reactome:R-HSA-8875451 Reactome:R-HSA-8875817 Reactome:R-HSA-8876230 Reactome:R-HSA-8876246 Reactome:R-HSA-8876948 Reactome:R-HSA-8937728 Reactome:R-HSA-8937807 Reactome:R-HSA-8937844 Reactome:R-HSA-8942607 Reactome:R-HSA-8948143 Reactome:R-HSA-8956659 Reactome:R-HSA-8964242 Reactome:R-HSA-8964252 Reactome:R-HSA-8983872 Reactome:R-HSA-9006323 Reactome:R-HSA-9006332 Reactome:R-HSA-9011241 Reactome:R-HSA-9012650 Reactome:R-HSA-9018572 Reactome:R-HSA-9021609 Reactome:R-HSA-9024726 Reactome:R-HSA-9026464 Reactome:R-HSA-9026502 Reactome:R-HSA-9026510 Reactome:R-HSA-9026579 Reactome:R-HSA-9026890 Reactome:R-HSA-9027272 Reactome:R-HSA-9027273 Reactome:R-HSA-9027425 Reactome:R-HSA-9028728 Reactome:R-HSA-9029151 Reactome:R-HSA-9029155 Reactome:R-HSA-9032426 Reactome:R-HSA-9032532 Reactome:R-HSA-9032601 Reactome:R-HSA-9032854 Reactome:R-HSA-9033284 Reactome:R-HSA-9034714 Reactome:R-HSA-9034814 Reactome:R-HSA-9034875 Reactome:R-HSA-9037040 Reactome:R-HSA-909718 Reactome:R-HSA-909726 Reactome:R-HSA-909729 Reactome:R-HSA-909730 Reactome:R-HSA-909732 Reactome:R-HSA-912629 Reactome:R-HSA-9603420 Reactome:R-HSA-9604767 Reactome:R-HSA-9606159 Reactome:R-HSA-9606162 Reactome:R-HSA-9606163 Reactome:R-HSA-9612085 Reactome:R-HSA-9612996 Reactome:R-HSA-9613023 Reactome:R-HSA-9624014 Reactome:R-HSA-9625487 Reactome:R-HSA-9634390 Reactome:R-HSA-9664261 Reactome:R-HSA-9664275 Reactome:R-HSA-9664278 Reactome:R-HSA-9664588 Reactome:R-HSA-9664976 Reactome:R-HSA-9665032 Reactome:R-HSA-9665389 Reactome:R-HSA-9665411 Reactome:R-HSA-9665704 Reactome:R-HSA-9665705 Reactome:R-HSA-9665709 Reactome:R-HSA-9666425 Reactome:R-HSA-9669890 Reactome:R-HSA-9669911 Reactome:R-HSA-9670412 Reactome:R-HSA-9670418 Reactome:R-HSA-9672173 Reactome:R-HSA-9672175 Reactome:R-HSA-9673756 Reactome:R-HSA-9673761 Reactome:R-HSA-9674558 Reactome:R-HSA-9674567 Reactome:R-HSA-9680248 Reactome:R-HSA-9695834 Reactome:R-HSA-9698003 Reactome:R-HSA-9698005 Reactome:R-HSA-9699578 Reactome:R-HSA-9700164 Reactome:R-HSA-9700168 Reactome:R-HSA-9700171 Reactome:R-HSA-9700175 Reactome:R-HSA-9700181 Reactome:R-HSA-9700186 Reactome:R-HSA-9700193 Reactome:R-HSA-9700647 Reactome:R-HSA-9701488 Reactome:R-HSA-9703437 Reactome:R-HSA-9703438 Reactome:R-HSA-9706344 Reactome:R-HSA-9706350 Reactome:R-HSA-9709918 Reactome:R-HSA-9712082 Reactome:R-HSA-9712085 Reactome:R-HSA-9712086 Reactome:R-HSA-9712087 Reactome:R-HSA-9726848 Reactome:R-HSA-9733314 Reactome:R-HSA-9733323 Reactome:R-HSA-9762209 Reactome:R-HSA-982807 Reactome:R-HSA-983703 Reactome:R-HSA-983707 Reactome:R-HSA-983709 protein-tyrosine kinase activity molecular_function GO:0004713 protein tyrosine kinase activity GO:0004713 Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate. RHEA:10596 Reactome:R-HSA-112333 SRC autophosphorylation is positively regulated by InlA-bound CDH1 Reactome:R-HSA-114600 Fyn/Lyn-mediated phosphorylation of FcR1 gamma Reactome:R-HSA-1168394 STAT5 tyrosine phosphorylation Reactome:R-HSA-1169421 Trans-autophosphorylation of activated ligand-responsive EGFR mutant dimers Reactome:R-HSA-1225952 Phosphorylation of SHC1 by ligand-responsive p-6Y-EGFR mutants Reactome:R-HSA-1225960 Phosphorylation of CBL by ligand-responsive p-6Y-EGFR mutants Reactome:R-HSA-1247844 Phosphorylation of PLCG1 by ligand-responsive p-6Y-EGFR mutants Reactome:R-HSA-1248655 Trans-autophosphorylation of EGFRvIII mutant dimers Reactome:R-HSA-1248694 Trans-autophosphorylation of ERBB2 homodimer Reactome:R-HSA-1250195 SHC1 phosphorylation by ERBB2 heterodimers Reactome:R-HSA-1250315 Trans-autophosphorylation of ERBB4 homodimers Reactome:R-HSA-1250348 Phosphorylation of SHC1 by ERBB4 homodimers Reactome:R-HSA-1251922 PLCG1 phosphorylation by p-EGFR:p-ERBB2 Reactome:R-HSA-1295540 IL7:p-Y449-IL7R:JAK1:IL2RG:p-JAK3:STAT5A,STAT5B phosphorylates STAT5 Reactome:R-HSA-1295609 SRC phosphorylates SPRY2 on Y55 and Y227 Reactome:R-HSA-1307963 Autocatalytic phosphorylation of BetaKlotho-bound FGFR4 Reactome:R-HSA-1433418 Phosphorylation of JAK2 Reactome:R-HSA-1433454 Phosphorylation of GAB2 by SFKs Reactome:R-HSA-1433488 Phosphorylation of SHP2 by SFKs Reactome:R-HSA-1433506 Phosphorylation of APS Reactome:R-HSA-1433542 Phosphorylation and activation of VAV1 Reactome:R-HSA-1470009 Phosphorylation of STATs Reactome:R-HSA-1472121 Phosphorylation of p-KIT on Y900 by Src kinases Reactome:R-HSA-1524186 Phosphorylation of PLCgamma by PDGFR Reactome:R-HSA-1671691 PRLR-bound STAT5 is phosphorylated Reactome:R-HSA-170070 Wee1-mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes Reactome:R-HSA-170156 Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes Reactome:R-HSA-170991 SRC-1 autophosphorylates Reactome:R-HSA-171011 Binding and activation of MAP Kinase Reactome:R-HSA-174164 Phosphorylation of Cyclin A:Cdk2 at Tyr 15 Reactome:R-HSA-177930 GAB1 phosphorylation by EGFR kinase Reactome:R-HSA-177934 EGFR autophosphorylation Reactome:R-HSA-177937 Phosphorylation of EGFR by SRC kinase Reactome:R-HSA-182969 Phosphorylation of CBL (EGFR:CBL) Reactome:R-HSA-183058 Phosphorylation of CBL (EGFR:GRB2:CBL) Reactome:R-HSA-1839065 Phosphorylation of cytosolic FGFR1 fusion dimers Reactome:R-HSA-1839067 Phosphorylation of BCR moiety of BCR-FGFR1 Reactome:R-HSA-1839098 Activated FGFR1 mutants and fusions phosphorylate PLCG1 Reactome:R-HSA-1839110 p-BCR-p-FGFR1 phosphorylates GAB2 Reactome:R-HSA-1839112 Phosphorylation of STAT5 by cytosolic FGFR1 fusions Reactome:R-HSA-186786 Autophosphorylation of PDGF beta receptors Reactome:R-HSA-1888198 FGFR1OP-FGFR1 phosphorylates STAT1 and STAT3 Reactome:R-HSA-190326 Autocatalytic phosphorylation of FGFR4 Reactome:R-HSA-190385 Autocatalytic phosphorylation of FGFR3b Reactome:R-HSA-190388 Autocatalytic phosphorylation of FGFR3c Reactome:R-HSA-190408 Autocatalytic phosphorylation of FGFR2b Reactome:R-HSA-190413 Autocatalytic phosphorylation of FGFR2c Reactome:R-HSA-190427 Autocatalytic phosphorylation of FGFR1b Reactome:R-HSA-190429 Autocatalytic phosphorylation of FGFR1c Reactome:R-HSA-191062 Autocatalytic phosphorylation of Klotho-bound FGFR1c Reactome:R-HSA-191636 Phosphorylation of Cx43 by c-src Reactome:R-HSA-1963581 Trans-autophosphorylation of p-Y877-ERBB2 heterodimers Reactome:R-HSA-1963582 Trans-autophosphorylation of ERBB2 heterodimers Reactome:R-HSA-1963586 SRC family kinases phosphorylate ERBB2 Reactome:R-HSA-1982066 Ligand-independent phosphorylation of overexpressed FGFR1 Reactome:R-HSA-2012073 Autocatalytic phosphorylation of FGFR3c P250R mutant Reactome:R-HSA-2012082 Autocatalytic phosphorylation of FGFR3 cysteine mutants Reactome:R-HSA-2012087 Autocatalytic phosphorylation of FGFR4 Y367C mutant Reactome:R-HSA-201521 ALK autophosphorylation downstream of PTN and MDK Reactome:R-HSA-202165 Phosphorylation of ITAM motifs in CD3 complexes Reactome:R-HSA-202168 Phosphorylation of ZAP-70 by Lck Reactome:R-HSA-202174 Activation of ZAP-70 Reactome:R-HSA-202216 Phosphorylation of SLP-76 Reactome:R-HSA-202233 Inactivation of Lck by Csk Reactome:R-HSA-202245 Phosphorylation of TBSMs in LAT Reactome:R-HSA-202248 Phosphorylation of PLC-gamma1 Reactome:R-HSA-202291 Activation of Lck Reactome:R-HSA-202307 Change of PKC theta conformation Reactome:R-HSA-2023455 Autocatalytic phosphorylation of FGFR1c P252X mutant dimers Reactome:R-HSA-2023460 Autocatalytic phosphorylation of FGFR1 mutants with enhanced kinase activity Reactome:R-HSA-2029268 Phosphorylation and activation of PLCG Reactome:R-HSA-2029449 Phosphorylation of SYK by Src kinases Reactome:R-HSA-2029453 Phosphorylation of VAV Reactome:R-HSA-2029459 Sequestering and phosphorylation Fc gamma receptors in the lipid rafts Reactome:R-HSA-2029984 Autocatalytic phosphorylation of FGFR2 ligand-independent mutants Reactome:R-HSA-2029989 Autocatalytic phosphorylation of overexpressed FGFR2 variants Reactome:R-HSA-2033485 Autocatalytic phosphorylation of FGFR3 point mutants with enhanced kinase activity Reactome:R-HSA-2033486 Autocatalytic phosphorylation of FGFR2c mutants with enhanced ligand binding Reactome:R-HSA-2033488 Autocatalytic phosphorylation of FGFR2b mutants with enhanced ligand binding Reactome:R-HSA-2033490 Autocatalytic phosphorylation of FGFR2 point mutants with enhanced kinase activity Reactome:R-HSA-2038387 Autocatalytic phosphorylation of FGFR3 t(4;14) translocation mutants Reactome:R-HSA-2038944 Autocatalytic phosphorylation of FGFR4 mutants with enhanced kinase activity Reactome:R-HSA-205289 Autophosphorylation of KIT Reactome:R-HSA-210291 Phosphorylation of PECAM-1 by Fyn or Lyn or c-Src Reactome:R-HSA-210872 Trans-phosphorylation of Tie2 Reactome:R-HSA-212710 EGFR activates PLC-gamma1 by phosphorylation Reactome:R-HSA-2130194 ABL phosphorylates WAVEs Reactome:R-HSA-2197698 Src phosphorylate WASP,N-WASP Reactome:R-HSA-2201322 TIRAP is phosphorylated by BTK Reactome:R-HSA-2395412 Phosphorylation of SYK Reactome:R-HSA-2395439 Phosphorylation of DAP12 Reactome:R-HSA-2395801 Phosphorylation of LAT by p-SYK Reactome:R-HSA-2396594 Phosphorylation of SLP-76 by p-SYK Reactome:R-HSA-2404193 IGF1R phosphorylates SHC1 Reactome:R-HSA-2404199 IGF1,2:IGF1R autophosphorylates Reactome:R-HSA-2424484 Phosphorylation of BTK by p-SYK Reactome:R-HSA-2424486 Phosphorylation and activation of VAV2/VAV3 by SYK Reactome:R-HSA-2424487 Phosphorylation of PLC-gamma by p-BTK/p-SYK Reactome:R-HSA-2428926 IGF1,2:p-Y1161,1165,1166-IGF1R phosphorylates IRS1,2,4 Reactome:R-HSA-2454208 Phosphorylation of beta and gamma subunits by LYN Reactome:R-HSA-2454239 Phosphorylation of SYK Reactome:R-HSA-2586553 JAK2 Phosphorylates LEPR Reactome:R-HSA-2586555 JAK2 Autophosphorylates in Response to Leptin Reactome:R-HSA-2671742 JAK2 Phosphorylates SHP2 (PTPN11) in Response to Leptin Reactome:R-HSA-2671829 JAK2 Phosphorylates STAT5 in Response to Leptin Reactome:R-HSA-2671850 JAK2 Phosphoryates STAT3 in Response to Leptin Reactome:R-HSA-2730833 Phosphorylation of TEC kinases by p-SYK Reactome:R-HSA-2730843 Phosphorylation of LAT by p-SYK Reactome:R-HSA-2730851 Phosphorylation of SLP-76 by p-SYK Reactome:R-HSA-2730858 Autophosphorylation of BTK/ITK Reactome:R-HSA-2730860 Phosphorylation of GAB2 by SYK/FYN Reactome:R-HSA-2730862 Autophosphorylation of LYN kinase Reactome:R-HSA-2730882 Phosphorylation of PKC-theta Reactome:R-HSA-2730884 Phosphorylation of NTAL by p-SYK/Lyn Reactome:R-HSA-2730886 Phosphorylation of SHC by SYK kinase Reactome:R-HSA-2730888 Phosphorylation of PLC-gamma Reactome:R-HSA-3215391 PRMT5 is tyrosine phosphorylated by JAK2 V617F Reactome:R-HSA-354073 Autophosphorylation of PTK2 at Y397 Reactome:R-HSA-354124 Phosphorylation of pPTK2 by SRC Reactome:R-HSA-372693 Phosphorylation of BCAR1 by SRC-PTK2 complex Reactome:R-HSA-373747 Phosphorylation of nephrin by FYN Reactome:R-HSA-373750 SEMA4D interacts with Plexin-B1:ErbB2 Reactome:R-HSA-374701 Phosphorylation of DCC by Fyn Reactome:R-HSA-377640 Autophosphorylation of SRC Reactome:R-HSA-380780 Activation of Src Reactome:R-HSA-388831 Phosphorylation of CD28 Reactome:R-HSA-388833 Phosphorylation of CTLA-4 Reactome:R-HSA-389083 Autophosphorylation of PDGF alpha receptors Reactome:R-HSA-389086 Autophosphorylation of PDGF alpha/beta receptors Reactome:R-HSA-389159 CSF1R trans-autophosphorylates on multiple tyrosine and serine residues Reactome:R-HSA-389354 Activation of Vav1 Reactome:R-HSA-389762 Phosphorylation of PD-1 Reactome:R-HSA-391156 Phosphorylation of ITIM motif in SIRP alpha Reactome:R-HSA-391865 Recruitment of FAK to NCAM1:Fyn in lipid rafts Reactome:R-HSA-391866 Phosphorylation of FAK by Src kinase Reactome:R-HSA-391871 Autophosphorylation of NCAM1 bound Fyn Reactome:R-HSA-3928578 EPH receptors autophosphorylate Reactome:R-HSA-3928580 SFKs phosphorylate EFNBs Reactome:R-HSA-3928583 FYN phosphorylates NMDAR2B Reactome:R-HSA-3928594 SFKs phosphorylate GIT1 Reactome:R-HSA-3928604 SFKs phosphorylate VAV2,3 Reactome:R-HSA-3928610 PTK2 autophosphorylates at Y397 Reactome:R-HSA-3928627 EPHB phosphorylates TIAM1 Reactome:R-HSA-3928648 SFKs phosphorylate NGEF Reactome:R-HSA-399934 Phosphorylation of Plexin-A Reactome:R-HSA-399946 Recruitment and activation of Cdk5 Reactome:R-HSA-399947 Tyrosine phosphorylation of CRMPs by Fes Reactome:R-HSA-4093332 p-EPHB phosphorylates SDC2 Reactome:R-HSA-418163 Activated SRC-1 activates MAPKs (in F2R:ARRB1:MAPKs:active SRC-1) Reactome:R-HSA-418859 Phosphorylation of Unc5C Reactome:R-HSA-418872 Phosphorylation of FADK1 Reactome:R-HSA-419646 SEMA4D interacts with Plexin-B1:Met Reactome:R-HSA-428888 Phosphorylation of ROBO1 by ABL kinase Reactome:R-HSA-429441 SYK activation by SRC Reactome:R-HSA-429449 Syk activation leads to SLP-76 activation Reactome:R-HSA-432129 FGR binds and phosphorylates LRP8 Reactome:R-HSA-434836 Syk/Lck phosphorylate LAT Reactome:R-HSA-4420117 VEGFR2 autophosphorylates Reactome:R-HSA-4420121 SFKs phosphorylate PLCG1 Reactome:R-HSA-4420128 SRC-1 phosphorylates SHB Reactome:R-HSA-4420206 Phosphorylation of SRC-1 Reactome:R-HSA-443817 Phosphorylation of L1 by EPHB2 Reactome:R-HSA-445076 Phosphorylation of Y1229 in L1 Reactome:R-HSA-445084 Phosphorylation of L1 by SRC Reactome:R-HSA-445085 Phosphorylation of VAV2 Reactome:R-HSA-445091 Phosphorylation of Neurofascin Reactome:R-HSA-451942 Within the IL-2R complex JAK3 phosphorylates JAK1 Reactome:R-HSA-452097 Recruited STAT5 is phosphorylated Reactome:R-HSA-452100 SHC1 bound to IL2 receptor is phosphorylated Reactome:R-HSA-452122 JAK1 phosphorylates Y338, Y392 and Y510 of IL2RB Reactome:R-HSA-508282 SYK is a substrate for JAK1 Reactome:R-HSA-5218640 SRC-1 phosphorylates p-Y397-PTK2 Reactome:R-HSA-5218642 PTK2 autophosphorylates Reactome:R-HSA-5218806 FYN autophosphorylates Reactome:R-HSA-5218809 PTK2 and SRC-1 phosphorylate PXN on Y31 and Y118 Reactome:R-HSA-5218812 FYN phosphorylates PAK2 Reactome:R-HSA-5218820 Src kinases phosphorylate VAV Reactome:R-HSA-5218828 PTK2/SRC-1 phosphorylates BCAR1 Reactome:R-HSA-5218830 SRC-1 phosphorylates PTK2-beta Reactome:R-HSA-5218851 p-Y402-PTK2B phosphorylates p-5Y,S732-PTK2 on Y407 Reactome:R-HSA-5357429 AXL autophosphorylates on Y772 and Y814 Reactome:R-HSA-5607745 1,3-beta-D-glucan:p-Y15-CLEC7A:SYK phosphorylates PLCG Reactome:R-HSA-5607750 SRC kinase phosphorylates CLEC7A:1,3-beta-D-glucan Reactome:R-HSA-5621355 LYN and FYN phosphorylate FCER1G in CLEC6A:FCERG and CLEC4E:FCERG Reactome:R-HSA-5621363 SYK phosphorylates PLCG2 in p-6Y-SYK:p-Y65,Y76-FCER1G:PLCG2 Reactome:R-HSA-5621370 SYK autophosphorylates Reactome:R-HSA-5624486 SFKs phosphorylates RAF1 on Y340,Y341 Reactome:R-HSA-5637795 Phosphorylation of PLC-gamma 1 by p-EGFRvIII mutant Reactome:R-HSA-5637796 Phosphorylation of SHC1 by p-5Y-EGFRvIII Reactome:R-HSA-5654147 Activated FGFR2 phosphorylates PLCG1 Reactome:R-HSA-5654149 Activated FGFR1 phosphorylates PLCG1 Reactome:R-HSA-5654151 Activated FGFR4 phosphorylates PLCG1 Reactome:R-HSA-5654222 Activated FGFR3 phosphorylates PLCG1 Reactome:R-HSA-5654397 Activated FGFR2 phosphorylates FRS2 Reactome:R-HSA-5654407 Activated FGFR2 phosphorylates SHC1 Reactome:R-HSA-5654408 Activated FGFR3 phosphorylates FRS2 Reactome:R-HSA-5654418 Activated FGFR4 phosphorylates FRS2 Reactome:R-HSA-5654428 Activated FGFR4 phosphorylates SHC1 Reactome:R-HSA-5654545 Ligand-independent phosphorylation of overexpressed FGFR1c Reactome:R-HSA-5654575 Activated FGFR1 phosphorylates FRS2 Reactome:R-HSA-5654578 Activated FGFR1 phosphorylates FRS3 Reactome:R-HSA-5654582 Activated FGFR1 phosphorylates SHC1 Reactome:R-HSA-5654587 Activated FGFR1:p-FRS phosphorylates PPTN11 Reactome:R-HSA-5654605 Activated FGFR2 phosphorylates FRS3 Reactome:R-HSA-5654607 Activated FGFR2 phosphorylates PPTN11 Reactome:R-HSA-5654628 Activated FGFR3 phosphorylates FRS3 Reactome:R-HSA-5654631 Activated FGFR3 phosphorylates PPTN11 Reactome:R-HSA-5654634 Activated FGFR3 phosphorylates SHC1 Reactome:R-HSA-5654653 Activated FGFR4 phosphorylates FRS3 Reactome:R-HSA-5654655 Activated FGFR4 phosphorylates PPTN11 Reactome:R-HSA-5655243 Activated FGFR3 point and translocation mutants phosphorylate PLCG1 Reactome:R-HSA-5655268 Activated FGFR2 mutants phosphorylate FRS2 Reactome:R-HSA-5655270 Activated FGFR3 point, translocation and fusion mutants phosphorylate FRS2 Reactome:R-HSA-5655278 Activated FGFR1 mutants phosphorylate FRS2 Reactome:R-HSA-5655284 Activated FGFR4 mutants phosphorylate FRS2 Reactome:R-HSA-5655301 Activated FGFR2 mutants phosphorylate PLCG1 Reactome:R-HSA-5655341 Activated FGFR4 mutants phosphorylate PLCG1 Reactome:R-HSA-5683930 WICH phosphorylates H2AFX on Y142 Reactome:R-HSA-5686587 ABL1 phosphorylates RAD52 Reactome:R-HSA-5690702 LYN phosphorylates CD22 Reactome:R-HSA-6784006 STAT3 is phosphorylated by p-Y-JAK1,P-Y-TYK2 Reactome:R-HSA-6784319 JAK1,TYK2 phosphorylate JAK1,TYK2 Reactome:R-HSA-6790087 HVEM induses BTLA phosphorylation Reactome:R-HSA-6806974 MET dimers autophosphorylate Reactome:R-HSA-68954 Mcm2-7 is phosphorylated by DDK Reactome:R-HSA-69195 Phosphorylation of Cyclin E:CDK2 complexes by WEE1 Reactome:R-HSA-873918 Transphosphorylation of JAK1 Reactome:R-HSA-873919 Phosphorylation of JAK2 Reactome:R-HSA-873922 Phosphorylation of STAT1 by JAK kinases Reactome:R-HSA-873924 Phosphorylation of IFNGR1 by JAK kinases Reactome:R-HSA-879907 Tyrosine kinases phosphorylate the receptor Reactome:R-HSA-879909 Activation of STAT5a/b by JAK2 Reactome:R-HSA-879925 SHC1 bound to the common beta chain becomes tyrosine phosphorylated Reactome:R-HSA-8847977 FRK phosphorylates PTEN Reactome:R-HSA-8848005 ERBB2 promotes PTK6 autophosphorylation Reactome:R-HSA-8848077 PTK6 phosphorylates STAP2 Reactome:R-HSA-8848124 PTK6 phosphorylates STAT3 Reactome:R-HSA-8848436 PTK6 phosphorylates CDKN1B Reactome:R-HSA-8848606 PTK6 phosphorylates PXN Reactome:R-HSA-8848726 PTK6 phosphorylates BCAR1 Reactome:R-HSA-8848758 PTK6 phosphorylates AKT1 Reactome:R-HSA-8848776 PTK6 phosphorylates DOK1 Reactome:R-HSA-8848818 PTK6 phosphorylates CBL Reactome:R-HSA-8848873 PTK6 phosphorylates ARAP1 Reactome:R-HSA-8848975 PTK6 phosphorylates KHDRBS1 Reactome:R-HSA-8849032 PTK6 phosphorylates KHDRBS2 Reactome:R-HSA-8849042 PTK6 phosphorylates KHDRBS3 Reactome:R-HSA-8849068 PTK6 phosphorylates ARHGAP35 Reactome:R-HSA-8849102 SRMS phosphorylates PTK6 Reactome:R-HSA-8849463 PTK6 phosphorylates SFPQ Reactome:R-HSA-8851890 MET phosphorylates SHC1-2 Reactome:R-HSA-8851933 MET phosphorylates GAB1 Reactome:R-HSA-8853309 Autocatalytic phosphorylation of FGFR3 fusions Reactome:R-HSA-8853313 FGFR2 fusions autophosphorylate Reactome:R-HSA-8853325 Plasma membrane FGFR1 fusions autophosphorylate Reactome:R-HSA-8855237 FYN phosphorylates DAB1 in RELN:VLDLR:DAB1:SH3KBP1 Reactome:R-HSA-8857555 EGFR phosphorylates GPNMB Reactome:R-HSA-8857577 LINC01139 facilitates PTK6 autophosphorylation Reactome:R-HSA-8857583 LINC01139 promotes phosphorylation of HIF1A by PTK6 Reactome:R-HSA-8857925 Inhibition of PP2A activity by phosphorylation of the catalytic subunit at tyrosine Y307 Reactome:R-HSA-8867041 EGFR phosphorylates EPS15 Reactome:R-HSA-8874078 PTK2 autophosphorylates Reactome:R-HSA-8874080 SRC phosphorylates PTK2 Reactome:R-HSA-8874082 MET phosphorylates PTK2 Reactome:R-HSA-8875451 MET phosphorylates CBL Reactome:R-HSA-8875817 MET phosphorylates STAT3 Reactome:R-HSA-8876230 InlB:MET dimer trans-autophophorylates Reactome:R-HSA-8876246 InlB-activated MET phosphorylates CBL Reactome:R-HSA-8876948 SRC phosphorylates InlA-bound CDH1 and CTNNB1 Reactome:R-HSA-8937728 SRC phosphorylates RUNX1 Reactome:R-HSA-8937807 SRC phosphorylates RUNX3 Reactome:R-HSA-8937844 SRC,YES1 phosphorylate YAP1 Reactome:R-HSA-8942607 Tyrosine kinases phosphorylate Cip/Kip inhibitors bound to CDK4/6:CCND complexes Reactome:R-HSA-8948143 p-S13, FUNDC1 is phosphorylated by CK2 at Tyr18 Reactome:R-HSA-8956659 ABL1 phosphorylates YAP1 Reactome:R-HSA-8964242 G protein alpha (i)-SRC complex catalyzes SRC to p-Y416-SRC Reactome:R-HSA-8964252 G alpha (s):GTP:SRC catalyzes SRC to p-Y416-SRC Reactome:R-HSA-8983872 JAK2 bound to IL12RB2:IL12RB2 phosphorylate STAT4 Reactome:R-HSA-9006323 Phospho-JAK2 phosphorylates EPOR Reactome:R-HSA-9006332 JAK2 transphosphorylates and is activated in response to Erythropoietin Reactome:R-HSA-9011241 SRC phosphorylates ROBO3.1 in response to NTN1 Reactome:R-HSA-9012650 JAK2 and LYN phosphorylate STAT5 in EPO:phospho-EPOR:phospho-JAK2:LYN:IRS2 Reactome:R-HSA-9018572 EGFR phosphorylates NOTCH3 Reactome:R-HSA-9021609 ESR-associated SRC autophosphorylates Reactome:R-HSA-9024726 LYN phosphorylates CRKL in EPO:p-8Y-EPOR:p-12Y-JAK2:LYN:IRS2:CRKL:RAPGEF1 Reactome:R-HSA-9026464 BDNF-bound NTRK2 dimers trans-autophosphorylate Reactome:R-HSA-9026502 NTF3-bound NTRK2 dimers trans-autophosphorylate Reactome:R-HSA-9026510 NTF4-bound NTRK2 dimers trans-autophosphorylate Reactome:R-HSA-9026579 NTRK2 phosphorylates PLCG1 Reactome:R-HSA-9026890 NTRK2 phosphorylates SHC1 Reactome:R-HSA-9027272 EPO:phospho-EPOR:phospho-JAK2:LYN:IRS2 phosphorylates IRS2 Reactome:R-HSA-9027273 JAK2 phosphorylates GAB1 in EPO:phospho-EPOR:phospho-JAK2:LYN:IRS2:GAB1 Reactome:R-HSA-9027425 LYN phosphorylates PLCG1,2 in EPO:phospho-EPOR:phospho-JAK2:LYN:IRS2:PLCG1,2 Reactome:R-HSA-9028728 NTRK2 phosphorylates FRS2 Reactome:R-HSA-9029151 JAK2 phosphorylates VAV1 in EPO:p-8Y-EPOR:p-12Y-JAK2:LYN:IRS2:p-Y-CRKL:RASGEF1:p-Y-SHC1:GRB2:VAV1 Reactome:R-HSA-9029155 JAK2 phosphorylates SHC1 in EPO:p-8Y-EPOR:p-12Y-JAK2:LYN:p-CRKL:RABGEF1:SHC1 Reactome:R-HSA-9032426 NTRK2 phosphorylates FRS3 Reactome:R-HSA-9032532 NTRK2-bound FYN autophosphorylates Reactome:R-HSA-9032601 FYN-mediated phosphorylation of GRIN2B Reactome:R-HSA-9032854 NTRK2 phosphorylates CDK5 Reactome:R-HSA-9033284 NTRK2 promotes TIAM1 phosphorylation Reactome:R-HSA-9034714 NTRK3 dimers trans-autophosphorylate Reactome:R-HSA-9034814 NTRK3 phosphorylates PLCG1 Reactome:R-HSA-9034875 NTRK3 phosphorylates SHC1 Reactome:R-HSA-9037040 SRC,FYN phosphorylate NTRK2 Reactome:R-HSA-909718 Formation of p-STAT1 homodimer Reactome:R-HSA-909726 Phosphorylation of STAT1 Reactome:R-HSA-909729 Activation of JAK kinases Reactome:R-HSA-909730 Phosphorylation of INFAR1 by TYK2 Reactome:R-HSA-909732 Phosphorylation of STAT2 Reactome:R-HSA-912629 CBL is tyrosine phosphorylated Reactome:R-HSA-9603420 Activated NTRK3 promotes SRC autophosphorylation Reactome:R-HSA-9604767 FLT3LG dimer:FLT3 dimer autophosphorylates Reactome:R-HSA-9606159 BTK autophosphorylates Reactome:R-HSA-9606162 Phosphorylated BTK phosphorylates PLCG2 Reactome:R-HSA-9606163 p-SYK and LYN phosphorylate BTK Reactome:R-HSA-9612085 SRC phosphorylates GluN2 (GRIN2) subunits of NMDARs Reactome:R-HSA-9612996 NTRK1,2 in ADCYAP1(2-742):ADCYAP1R1:NTRK1,2 autophosphorylates Reactome:R-HSA-9613023 NTRK1,2 in Ade-Rib:ADORA2A:NTRK1,2 autophosphorylates Reactome:R-HSA-9624014 SHC1 is phosphorylated downstream of estrogen stimulation of GPER1 Reactome:R-HSA-9625487 PTK2 autophosphorylates downstream of EGFR Reactome:R-HSA-9634390 ERBB2 homodimer phosphorylates SHC1 Reactome:R-HSA-9664261 Src phosphorylate SYK in IgG:Leishmania surface:p-FCGR3A:SYK Reactome:R-HSA-9664275 Src phosphorylates CD3 dimers in IgG:Lma antigens:FCGR3A:CD3 dimers Reactome:R-HSA-9664278 Phosphorylation and activation of PLCG due to FCGR3A effect Reactome:R-HSA-9664588 ERBB2 KD mutants trans-autophosphorylate Reactome:R-HSA-9664976 Phosphorylated heterodimers of ERBB2 KD mutants phosphorylate SHC1 Reactome:R-HSA-9665032 Phosphorylated heterodimers of ERBB2 KD mutants and EGFR phosphorylate PLCG1 Reactome:R-HSA-9665389 Heterodimers of ERBB2 ECD mutants and EGFR trans-autophosphorylate Reactome:R-HSA-9665411 Phosphorylated heterodimers of ERBB2 ECD mutants and EGFR phosphorylate PLCG1 Reactome:R-HSA-9665704 Phosphorylated heterodimers of ERBB2 TMD/JMD mutants and EGFR phosphorylate PLCG1 Reactome:R-HSA-9665705 Phosphorylated heterodimers of ERBB2 TMD/JMD mutants phosphorylate SHC1 Reactome:R-HSA-9665709 ERBB2 TMD/JMD heterodimers trans-autophosphorylate Reactome:R-HSA-9666425 p-6Y-SYK phosphorylates VAV1,2,3 Reactome:R-HSA-9669890 Constitutive phosphorylation of kinase domain KIT mutants Reactome:R-HSA-9669911 Phosphorylation of juxtamembrane domain KIT mutants Reactome:R-HSA-9670412 Phosphorylation of STATs downstream of KIT mutants Reactome:R-HSA-9670418 Phosphorylation of JAK2 downstream of KIT mutants Reactome:R-HSA-9672173 Autophosphorylation of PDGFRA extracellular domain dimers Reactome:R-HSA-9672175 Autophosphorylation of PDGFR mutant dimers Reactome:R-HSA-9673756 Autophosphorylation of cytosolic PDGFRA and PDGFRB fusion proteins Reactome:R-HSA-9673761 Autophosphorylation of membrane-tethered fusions of PDGFRA or PDGFRB Reactome:R-HSA-9674558 p-Y-JAK1 phosphorylates CSF3R in CSF3 dimer:2xCSF3R:LYN:p-Y-JAK1 Reactome:R-HSA-9674567 p-Y-JAK1,2 phosphorylates STAT1,3,5 in CSF3 dimer:2xp-4Y-CSF3R:LYN:p-Y-JAK1:p-Y-JAK2:p-TYK2 Reactome:R-HSA-9680248 Phosphorylation of extracellular domain KIT mutants Reactome:R-HSA-9695834 Constitutive phosphorylation of FLT3 mutants Reactome:R-HSA-9698003 FLT3 mutants phosphorylate GAB2 Reactome:R-HSA-9698005 FLT3 ITD mutants phosphorylate STAT5 Reactome:R-HSA-9699578 Active FLT3 phosphorylates CDKN1B Reactome:R-HSA-9700164 Active ALK phosphorylates FRS2 Reactome:R-HSA-9700168 Active ALK phosphorylates IRS1 Reactome:R-HSA-9700171 Active ALK phosphorylates PLCG1 Reactome:R-HSA-9700175 Active ALK phosphorylates SHC1 Reactome:R-HSA-9700181 Autophosphorylation of ALK fusions Reactome:R-HSA-9700186 Autophosphorylation of point mutants of ALK Reactome:R-HSA-9700193 ALK mutants phosphorylate SHC1 Reactome:R-HSA-9700647 Active ALK phosphorylates SRC Reactome:R-HSA-9701488 Active ALK phosphorylates JAK3 Reactome:R-HSA-9703437 FLT3 fusion dimers autophosphorylate Reactome:R-HSA-9703438 FLT3 fusions phosphorylate GAB2 Reactome:R-HSA-9706344 FLT3 phosphorylates GRB10 Reactome:R-HSA-9706350 FLT3 phosphorylates CBL Reactome:R-HSA-9709918 PTK6 phosphorylates STAT3 Reactome:R-HSA-9712082 ALK fusions phosphorylate IRS1 Reactome:R-HSA-9712085 ALK mutants phosphorylate STAT3 Reactome:R-HSA-9712086 ALK fusions phosphorylate PLCG1 Reactome:R-HSA-9712087 ALK fusions phosphorylate FRS Reactome:R-HSA-9726848 SRC phosphorylates RHOU Reactome:R-HSA-9733314 CSF1R trans-autophosphorylates on tyrosine-561 Reactome:R-HSA-9733323 Src family kinases phosphorylate CBL in CSF1 dimer:p-Y561-CSF1R dimer:CBL Reactome:R-HSA-9762209 BACH1 is phosphorylated at tyrosine 486 Reactome:R-HSA-982807 JAK2 phosphorylation of GHR Reactome:R-HSA-983703 p-6Y-SYK phosphorylates BLNK (SLP65) Reactome:R-HSA-983707 SYK autophosphorylates at the activated BCR Reactome:R-HSA-983709 LYN, FYN, BLK phosphorylate ITAMs of Ig-alpha (CD79A) and Ig-beta (CD79B) Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cellular proteins and thereby provide an important mechanism for regulating cellular activity. MetaCyc:3.1.3.16-RXN Reactome:R-HSA-112383 Reactome:R-HSA-113503 Reactome:R-HSA-1363274 Reactome:R-HSA-1363276 Reactome:R-HSA-167072 Reactome:R-HSA-170153 Reactome:R-HSA-170158 Reactome:R-HSA-170161 Reactome:R-HSA-174110 Reactome:R-HSA-174124 Reactome:R-HSA-178178 Reactome:R-HSA-2529015 Reactome:R-HSA-69199 Reactome:R-HSA-9636684 phosphoprotein phosphohydrolase activity protein phosphatase activity protein phosphatase-1 activity protein phosphatase-2A activity protein phosphatase-2B activity protein phosphatase-2C activity molecular_function GO:0004721 phosphoprotein phosphatase activity GO:0004721 Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cellular proteins and thereby provide an important mechanism for regulating cellular activity. ISBN:0198547684 Reactome:R-HSA-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein Reactome:R-HSA-113503 PP2A mediated localization of RB1 protein in chromatin Reactome:R-HSA-1363274 Dephosphorylation of p107 (RBL1) by PP2A Reactome:R-HSA-1363276 Dephosphorylation of p130 (RBL2) by PP2A Reactome:R-HSA-167072 Hypophosphorylation of RNA Pol II CTD by FCP1P protein Reactome:R-HSA-170153 Dephosphorylation of nuclear Cyclin B1:phospho-Cdc2 (Thr 14, Tyr15) complexes by Cdc25 phosphatases Reactome:R-HSA-170158 Dephosphorylation of nuclear Cyclin A:phospho-Cdc2 complexes Reactome:R-HSA-170161 Dephosphorylation of cytoplasmic Cyclin B1/B2:phospho-Cdc2 (Thr 14, Tyr 15) complexes by CDC25B Reactome:R-HSA-174110 Cdc25A mediated dephosphorylation of Cyclin A:phospho-Cdk2 Reactome:R-HSA-174124 Dephosphorylation of phospho-Cdh1 Reactome:R-HSA-178178 PP1 dephosphorylates TGFBR1 Reactome:R-HSA-2529015 Dephosphorylation of CK2-modified condensin I Reactome:R-HSA-69199 Dephosphorylation of Cyclin E:Cdk2 complexes by Cdc25A Reactome:R-HSA-9636684 ndkA dephosphorylates RAB5A:GTP,RAB7A:GTP Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. E2 E3 KEGG_REACTION:R03876 Reactome:R-HSA-1169394 Reactome:R-HSA-1169395 Reactome:R-HSA-1169397 Reactome:R-HSA-1169398 Reactome:R-HSA-1169402 Reactome:R-HSA-1169405 Reactome:R-HSA-1169406 Reactome:R-HSA-1234163 Reactome:R-HSA-1234172 Reactome:R-HSA-1253282 Reactome:R-HSA-1358789 Reactome:R-HSA-1358790 Reactome:R-HSA-1358792 Reactome:R-HSA-1363331 Reactome:R-HSA-168915 Reactome:R-HSA-173542 Reactome:R-HSA-173545 Reactome:R-HSA-174057 Reactome:R-HSA-174104 Reactome:R-HSA-174144 Reactome:R-HSA-174159 Reactome:R-HSA-174195 Reactome:R-HSA-174227 Reactome:R-HSA-179417 Reactome:R-HSA-180540 Reactome:R-HSA-180597 Reactome:R-HSA-182986 Reactome:R-HSA-182993 Reactome:R-HSA-183036 Reactome:R-HSA-183051 Reactome:R-HSA-183084 Reactome:R-HSA-183089 Reactome:R-HSA-1852623 Reactome:R-HSA-187575 Reactome:R-HSA-1912357 Reactome:R-HSA-1912386 Reactome:R-HSA-1918092 Reactome:R-HSA-1918095 Reactome:R-HSA-1977296 Reactome:R-HSA-1980074 Reactome:R-HSA-1980118 Reactome:R-HSA-201425 Reactome:R-HSA-202453 Reactome:R-HSA-202534 Reactome:R-HSA-205118 Reactome:R-HSA-209063 Reactome:R-HSA-211734 Reactome:R-HSA-2169050 Reactome:R-HSA-2172172 Reactome:R-HSA-2179276 Reactome:R-HSA-2186747 Reactome:R-HSA-2186785 Reactome:R-HSA-2187368 Reactome:R-HSA-2213017 Reactome:R-HSA-264444 Reactome:R-HSA-2682349 Reactome:R-HSA-2730904 Reactome:R-HSA-2737728 Reactome:R-HSA-2769007 Reactome:R-HSA-2900765 Reactome:R-HSA-3000335 Reactome:R-HSA-3134804 Reactome:R-HSA-3134946 Reactome:R-HSA-3249386 Reactome:R-HSA-3780995 Reactome:R-HSA-3781009 Reactome:R-HSA-3788724 Reactome:R-HSA-3797226 Reactome:R-HSA-400267 Reactome:R-HSA-4332236 Reactome:R-HSA-446877 Reactome:R-HSA-450358 Reactome:R-HSA-451418 Reactome:R-HSA-5205682 Reactome:R-HSA-5357757 Reactome:R-HSA-5362412 Reactome:R-HSA-5483238 Reactome:R-HSA-5607725 Reactome:R-HSA-5607728 Reactome:R-HSA-5607756 Reactome:R-HSA-5607757 Reactome:R-HSA-5610742 Reactome:R-HSA-5610745 Reactome:R-HSA-5610746 Reactome:R-HSA-5652009 Reactome:R-HSA-5655170 Reactome:R-HSA-5660753 Reactome:R-HSA-5667107 Reactome:R-HSA-5667111 Reactome:R-HSA-5668454 Reactome:R-HSA-5668534 Reactome:R-HSA-5675470 Reactome:R-HSA-5684250 Reactome:R-HSA-5691108 Reactome:R-HSA-5693108 Reactome:R-HSA-68712 Reactome:R-HSA-69598 Reactome:R-HSA-741386 Reactome:R-HSA-75824 Reactome:R-HSA-870449 Reactome:R-HSA-8948709 Reactome:R-HSA-8956106 Reactome:R-HSA-9013069 Reactome:R-HSA-9013974 Reactome:R-HSA-9014342 Reactome:R-HSA-918224 Reactome:R-HSA-936412 Reactome:R-HSA-936942 Reactome:R-HSA-936986 Reactome:R-HSA-9628444 Reactome:R-HSA-9645394 Reactome:R-HSA-9645414 Reactome:R-HSA-9688831 Reactome:R-HSA-9701000 Reactome:R-HSA-9750946 Reactome:R-HSA-975118 Reactome:R-HSA-975147 Reactome:R-HSA-9758604 Reactome:R-HSA-9793444 Reactome:R-HSA-9793485 Reactome:R-HSA-9793679 Reactome:R-HSA-9796346 Reactome:R-HSA-9796387 Reactome:R-HSA-9796626 Reactome:R-HSA-9815507 Reactome:R-HSA-9817362 Reactome:R-HSA-983140 Reactome:R-HSA-983153 Reactome:R-HSA-983156 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity ubiquitin protein-ligase activity ubiquitin-conjugating enzyme activity GO:0004842 ubiquitin-protein transferase activity GO:0004842 Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. GOC:BioGRID GOC:jh2 PMID:9635407 Reactome:R-HSA-1169394 ISGylation of IRF3 Reactome:R-HSA-1169395 ISGylation of viral protein NS1 Reactome:R-HSA-1169397 Activation of ISG15 by UBA7 E1 ligase Reactome:R-HSA-1169398 ISGylation of host protein filamin B Reactome:R-HSA-1169402 ISGylation of E2 conjugating enzymes Reactome:R-HSA-1169405 ISGylation of protein phosphatase 1 beta (PP2CB) Reactome:R-HSA-1169406 ISGylation of host proteins Reactome:R-HSA-1234163 Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha Reactome:R-HSA-1234172 Nuclear VBC complex ubiquitinylates HIF-alpha Reactome:R-HSA-1253282 ERBB4 ubiquitination by WWP1/ITCH Reactome:R-HSA-1358789 Self-ubiquitination of RNF41 Reactome:R-HSA-1358790 RNF41 ubiquitinates ERBB3 Reactome:R-HSA-1358792 RNF41 ubiquitinates activated ERBB3 Reactome:R-HSA-1363331 Ubiquitination of p130 (RBL2) by SCF (Skp2) Reactome:R-HSA-168915 K63-linked ubiquitination of RIP1 bound to the activated TLR complex Reactome:R-HSA-173542 SMURF2 ubiquitinates SMAD2 Reactome:R-HSA-173545 Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling Reactome:R-HSA-174057 Multiubiquitination of APC/C-associated Cdh1 Reactome:R-HSA-174104 Ubiquitination of Cyclin A by APC/C:Cdc20 complex Reactome:R-HSA-174144 Ubiquitination of Securin by phospho-APC/C:Cdc20 complex Reactome:R-HSA-174159 Ubiquitination of Emi1 by SCF-beta-TrCP Reactome:R-HSA-174195 Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex Reactome:R-HSA-174227 Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex Reactome:R-HSA-179417 Multiubiquitination of Nek2A Reactome:R-HSA-180540 Multi-ubiquitination of APOBEC3G Reactome:R-HSA-180597 Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex Reactome:R-HSA-182986 CBL-mediated ubiquitination of CIN85 Reactome:R-HSA-182993 Ubiquitination of stimulated EGFR (CBL) Reactome:R-HSA-183036 Ubiquitination of stimulated EGFR (CBL:GRB2) Reactome:R-HSA-183051 CBL ubiquitinates Sprouty Reactome:R-HSA-183084 CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix Reactome:R-HSA-183089 CBL binds and ubiquitinates phosphorylated Sprouty Reactome:R-HSA-1852623 Ubiquitination of NICD1 by FBWX7 Reactome:R-HSA-187575 Ubiquitination of phospho-p27/p21 Reactome:R-HSA-1912357 ITCH ubiquitinates DTX Reactome:R-HSA-1912386 Ubiquitination of NOTCH1 by ITCH in the absence of ligand Reactome:R-HSA-1918092 CHIP (STUB1) mediates ubiquitination of ERBB2 Reactome:R-HSA-1918095 CUL5 mediates ubiquitination of ERBB2 Reactome:R-HSA-1977296 NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer Reactome:R-HSA-1980074 Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 Reactome:R-HSA-1980118 ARRB mediates NOTCH1 ubiquitination Reactome:R-HSA-201425 Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling Reactome:R-HSA-202453 Auto-ubiquitination of TRAF6 Reactome:R-HSA-202534 Ubiquitination of NEMO by TRAF6 Reactome:R-HSA-205118 TRAF6 polyubiquitinates NRIF Reactome:R-HSA-209063 Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex Reactome:R-HSA-211734 Ubiquitination of PAK-2p34 Reactome:R-HSA-2169050 SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7 Reactome:R-HSA-2172172 Ubiquitination of DLL/JAG ligands upon binding to NOTCH2 Reactome:R-HSA-2179276 SMURF2 monoubiquitinates SMAD3 Reactome:R-HSA-2186747 Ubiquitination of SKI/SKIL by RNF111/SMURF2 Reactome:R-HSA-2186785 RNF111 ubiquitinates SMAD7 Reactome:R-HSA-2187368 STUB1 (CHIP) ubiquitinates SMAD3 Reactome:R-HSA-2213017 Auto-ubiquitination of TRAF3 Reactome:R-HSA-264444 Autoubiquitination of phospho-COP1(Ser-387 ) Reactome:R-HSA-2682349 RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels Reactome:R-HSA-2730904 Auto-ubiquitination of TRAF6 Reactome:R-HSA-2737728 Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants Reactome:R-HSA-2769007 Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants Reactome:R-HSA-2900765 Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants Reactome:R-HSA-3000335 SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA Reactome:R-HSA-3134804 STING ubiquitination by TRIM32 or TRIM56 Reactome:R-HSA-3134946 DDX41 ubiquitination by TRIM21 Reactome:R-HSA-3249386 DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1 Reactome:R-HSA-3780995 NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2 Reactome:R-HSA-3781009 NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1 Reactome:R-HSA-3788724 Cdh1:APC/C ubiquitinates EHMT1 and EHMT2 Reactome:R-HSA-3797226 Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) Reactome:R-HSA-400267 BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins Reactome:R-HSA-4332236 CBL neddylates TGFBR2 Reactome:R-HSA-446877 TRAF6 is K63 poly-ubiquitinated Reactome:R-HSA-450358 Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation Reactome:R-HSA-451418 Pellino ubiquitinates IRAK1 Reactome:R-HSA-5205682 Parkin promotes the ubiquitination of mitochondrial substrates Reactome:R-HSA-5357757 BIRC(cIAP1/2) ubiquitinates RIPK1 Reactome:R-HSA-5362412 SYVN1 ubiquitinates Hh C-terminal fragments Reactome:R-HSA-5483238 Hh processing variants are ubiquitinated Reactome:R-HSA-5607725 SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP Reactome:R-HSA-5607728 beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex Reactome:R-HSA-5607756 TRAF6 oligomer autoubiquitinates Reactome:R-HSA-5607757 K63polyUb-TRAF6 ubiquitinates TAK1 Reactome:R-HSA-5610742 SCF(beta-TrCP) ubiquitinates p-GLI1 Reactome:R-HSA-5610745 SCF(beta-TrCP) ubiquitinates p-GLI2 Reactome:R-HSA-5610746 SCF(beta-TrCP) ubiquitinates p-GLI3 Reactome:R-HSA-5652009 RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA Reactome:R-HSA-5655170 RCHY1 monoubiquitinates POLH Reactome:R-HSA-5660753 SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA Reactome:R-HSA-5667107 SIAH1, SIAH2 ubiquitinate SNCAIP Reactome:R-HSA-5667111 PARK2 K63-Ubiquitinates SNCAIP Reactome:R-HSA-5668454 K63polyUb-cIAP1,2 ubiquitinates TRAF3 Reactome:R-HSA-5668534 cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK Reactome:R-HSA-5675470 BIRC2/3 (cIAP1/2) is autoubiquitinated Reactome:R-HSA-5684250 SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2 Reactome:R-HSA-5691108 SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2 Reactome:R-HSA-5693108 TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains Reactome:R-HSA-68712 The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 Reactome:R-HSA-69598 Ubiquitination of phosphorylated Cdc25A Reactome:R-HSA-741386 RIP2 induces K63-linked ubiquitination of NEMO Reactome:R-HSA-75824 Ubiquitination of Cyclin D1 Reactome:R-HSA-870449 TRIM33 monoubiquitinates SMAD4 Reactome:R-HSA-8948709 DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3 Reactome:R-HSA-8956106 VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha Reactome:R-HSA-9013069 Ubiquitination of DLL/JAG ligands upon binding to NOTCH3 Reactome:R-HSA-9013974 Auto-ubiquitination of TRAF3 within activated TLR3 complex Reactome:R-HSA-9014342 K63-linked ubiquitination of RIP1 bound to the activated TLR complex Reactome:R-HSA-918224 DDX58 is K63 polyubiquitinated Reactome:R-HSA-936412 RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS Reactome:R-HSA-936942 Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 Reactome:R-HSA-936986 Activated TRAF6 synthesizes unanchored polyubiquitin chains Reactome:R-HSA-9628444 Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation Reactome:R-HSA-9645394 Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation Reactome:R-HSA-9645414 Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer Reactome:R-HSA-9688831 STUB1 ubiquitinates RIPK3 at K55, K363 Reactome:R-HSA-9701000 BRCA1:BARD1 heterodimer autoubiquitinates Reactome:R-HSA-9750946 TRAF2,6 ubiquitinates NLRC5 Reactome:R-HSA-975118 TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex Reactome:R-HSA-975147 Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane Reactome:R-HSA-9758604 Ubiquitination of IKBKG by TRAF6 Reactome:R-HSA-9793444 ITCH polyubiquitinates MLKL at K50 Reactome:R-HSA-9793485 PRKN polyubiquitinates RIPK3 Reactome:R-HSA-9793679 LUBAC ubiquitinates RIPK1 at K627 Reactome:R-HSA-9796346 MIB2 ubiquitinates RIPK1 at K377, K604, K634 Reactome:R-HSA-9796387 STUB1 ubiquitinates RIPK1 at K571, K604, K627 Reactome:R-HSA-9796626 MIB2 ubiquitinates CFLAR Reactome:R-HSA-9815507 MIB2 ubiquitinates CYLD at K338, K530 Reactome:R-HSA-9817362 SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex Reactome:R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2 Reactome:R-HSA-983153 E1 mediated ubiquitin activation Reactome:R-HSA-983156 Polyubiquitination of substrate The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding GO:0005488 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Binding to a protein. GO:0001948 GO:0045308 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding GO:0005515 Binding to a protein. GOC:go_curators A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component GO:0005575 A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular anatomical structure GO:0005622 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus GO:0005634 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope GO:0005635 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. inner envelope NIF_Subcellular:sao1612527463 inner nuclear membrane nucleus inner membrane cellular_component GO:0005637 nuclear inner membrane GO:0005637 The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope. GOC:ma inner nuclear membrane GOC:kmv GOC:vw PMID:21411627 The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane. NIF_Subcellular:sao1455996588 Wikipedia:Nuclear_lamina cellular_component GO:0005652 nuclear lamina GO:0005652 The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane. ISBN:0198506732 ISBN:0716731363 That part of the nuclear content other than the chromosomes or the nucleolus. NIF_Subcellular:sao661522542 Wikipedia:Nucleoplasm cellular_component GO:0005654 nucleoplasm GO:0005654 That part of the nuclear content other than the chromosomes or the nucleolus. GOC:ma ISBN:0124325653 The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. Wikipedia:Replication_fork cellular_component replication focus GO:0005657 replication fork GO:0005657 The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. GOC:mah ISBN:0198547684 A multisubunit complex that is located at the replication origins of a chromosome in the nucleus. eukaryotic ORC nuclear ORC cellular_component GO:0005664 nuclear origin of replication recognition complex GO:0005664 A multisubunit complex that is located at the replication origins of a chromosome in the nucleus. GOC:elh A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. jl 2013-08-28T12:11:37Z GO:0044797 GO:0044798 cellular_component cytoplasmic transcription factor complex nuclear transcription factor complex transcription factor complex GO:0005667 transcription regulator complex GO:0005667 A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription. GOC:jl A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters. cellular_component GO:0005669 transcription factor TFIID complex GO:0005669 A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters. GOC:krc GOC:mah ISBN:0471953393 ISBN:0879695501 Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing. cellular_component GO:0005677 chromatin silencing complex GO:0005677 Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing. GOC:mah Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA. spliceosome Wikipedia:Spliceosome spliceosome complex cellular_component GO:0005681 spliceosomal complex GO:0005681 Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA. GOC:editors GOC:mah ISBN:0198547684 PMID:19239890 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible. Wikipedia:Polytene_chromosome cellular_component GO:0005700 polytene chromosome GO:0005700 A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible. ISBN:0198506732 Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3). https://github.com/geneontology/go-ontology/issues/23924 GO:0002137 GO:0031618 GO:0034507 GO:0062199 centric heterochromatin centromeric heterochromatin nuclear centric heterochromatin nuclear cluster nuclear pericentric heterochromatin cellular_component chromosome, centric outer repeat region chromosome, centromeric inner repeat region chromosome, centromeric outer repeat region GO:0005721 pericentric heterochromatin GO:0005721 Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3). PMID:12019236 PMID:20206496 PMID:21437270 PMID:22729156 PMID:9413993 centromeric heterochromatin GOC:dph Structures of variable diameter visible in the nucleoplasm by electron microscopy, mainly observed near the border of condensed chromatin. The fibrils are enriched in RNA, and are believed to be sites of pre-mRNA splicing and polyadenylylation representing the in situ form of nascent transcripts. cellular_component GO:0005726 perichromatin fibrils GO:0005726 Structures of variable diameter visible in the nucleoplasm by electron microscopy, mainly observed near the border of condensed chromatin. The fibrils are enriched in RNA, and are believed to be sites of pre-mRNA splicing and polyadenylylation representing the in situ form of nascent transcripts. PMID:14731598 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component GO:0005730 nucleolus GO:0005730 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. ISBN:0198506732 A region of a chromosome where nucleoli form during interphase, and where genes encoding the largest rRNA precursor transcript are tandemly arrayed. Wikipedia:Nucleolus_organizer_region NOR nucleolus organiser region cellular_component nucleolus organizer complex GO:0005731 nucleolus organizer region GO:0005731 A region of a chromosome where nucleoli form during interphase, and where genes encoding the largest rRNA precursor transcript are tandemly arrayed. PMID:14504406 Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. cellular_component GO:0005871 kinesin complex GO:0005871 Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work. GOC:mah http://www.proweb.org/kinesin//KinesinMotility.html http://www.proweb.org/kinesin//KinesinStructure.html Any multimeric complex connected to a microtubule. cellular_component GO:0005875 microtubule associated complex GO:0005875 Any multimeric complex connected to a microtubule. GOC:jl A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too. 1-phosphatidylinositol 3-kinase complex PI3K complex phosphoinositide 3-kinase complex PI3-kinase p85-subunit alpha- PI3-kinase p110 complex PIK3C3-PIK3R4 complex PIK3CA-PIK3R1 complex cellular_component GO:0005942 For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/ phosphatidylinositol 3-kinase complex GO:0005942 A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too. GOC:bf PMID:24587488 PI3-kinase p85-subunit alpha- PI3-kinase p110 complex CORUM:2575 PIK3C3-PIK3R4 complex CORUM:429 PIK3CA-PIK3R1 complex CORUM:439 An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins. CAMK2 calcium/calmodulin-dependent protein kinase complex cellular_component CaMKII GO:0005954 calcium- and calmodulin-dependent protein kinase complex GO:0005954 An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins. PMID:20668654 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 Any process that modulates the frequency, rate or extent of DNA replication. biological_process GO:0006275 regulation of DNA replication GO:0006275 Any process that modulates the frequency, rate or extent of DNA replication. GOC:go_curators The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. biological_process GO:0006304 DNA modification GO:0006304 The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. GOC:jl GOC:ma The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis. biological_process GO:0006305 DNA alkylation GO:0006305 The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis. ISBN:0716735970 The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Wikipedia:DNA_methylation biological_process GO:0006306 DNA methylation GO:0006306 The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GOC:ems ISBN:0198506732 The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA. https://github.com/geneontology/go-ontology/issues/22130 https://github.com/geneontology/go-ontology/issues/23549 GO:0006333 GO:0006336 GO:0016568 GO:0031497 GO:0034724 chromatin maintenance chromatin organisation establishment of chromatin architecture establishment or maintenance of chromatin architecture DNA replication-independent chromatin assembly DNA replication-independent chromatin organization DNA replication-independent nucleosome organisation DNA replication-independent nuclesome assembly chromatin assembly transcription-coupled nucleosome assembly biological_process chromatin assembly or disassembly chromatin assembly/disassembly chromatin modification GO:0006325 chromatin organization GO:0006325 The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA. PMID:20404130 chromatin organisation GOC:mah establishment of chromatin architecture GOC:mah establishment or maintenance of chromatin architecture GOC:mah A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. https://github.com/geneontology/go-ontology/issues/21732 https://github.com/geneontology/go-ontology/issues/21748 GO:0043044 chromatin modeling chromatin modelling chromatin remodelling ATP-dependent chromatin remodeling ATP-dependent chromatin remodelling biological_process GO:0006338 chromatin remodeling GO:0006338 A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. GOC:jid GOC:vw PMID:12042764 PMID:12697820 Repression of transcription by methylation of DNA, leading to the formation of heterochromatin. https://github.com/geneontology/go-ontology/issues/22047 https://github.com/geneontology/go-ontology/issues/23553 methylation-dependent chromatin silencing methylation-dependent heterochromatic silencing DNA methylation-dependent heterochromatin assembly biological_process GO:0006346 DNA methylation-dependent heterochromatin formation GO:0006346 Repression of transcription by methylation of DNA, leading to the formation of heterochromatin. GOC:mah The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. protein amino acid acetylation biological_process GO:0006473 protein acetylation GO:0006473 The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. GOC:ai protein amino acid acetylation GOC:bf The addition of an acetyl group to a non-terminal amino acid in a protein. biological_process GO:0006475 internal protein amino acid acetylation GO:0006475 The addition of an acetyl group to a non-terminal amino acid in a protein. GOC:mah The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. protein amino acid deacetylation biological_process GO:0006476 protein deacetylation GO:0006476 The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. GOC:ai protein amino acid deacetylation GOC:bf The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. protein amino acid methylation biological_process GO:0006479 protein methylation GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GOC:ai protein amino acid methylation GOC:bf The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. protein amino acid demethylation biological_process GO:0006482 protein demethylation GO:0006482 The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GOC:mah protein amino acid demethylation GOC:bf The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. Wikipedia:Proteolysis peptidolysis ATP-dependent proteolysis biological_process GO:0006508 This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing. proteolysis GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GOC:bf GOC:mah ATP-dependent proteolysis GOC:mah Addition of a single ubiquitin group to a protein. protein monoubiquitinylation protein monoubiquitylation biological_process GO:0006513 protein monoubiquitination GO:0006513 Addition of a single ubiquitin group to a protein. GOC:ai The directed movement of a protein from the cytoplasm to the nucleus. establishment of protein localization to nucleus protein import into cell nucleus protein nucleus import protein transport from cytoplasm to nucleus biological_process GO:0006606 protein import into nucleus GO:0006606 The directed movement of a protein from the cytoplasm to the nucleus. GOC:jl establishment of protein localization to nucleus GOC:mah The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process GO:0006725 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process GO:0006807 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport GO:0006810 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport GO:0006886 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al The directed movement of molecules between the nucleus and the cytoplasm. GO:0000063 nucleocytoplasmic shuttling biological_process GO:0006913 Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. nucleocytoplasmic transport GO:0006913 The directed movement of molecules between the nucleus and the cytoplasm. GOC:go_curators A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization GO:0006996 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization GO:0006997 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. biological_process GO:0007076 mitotic chromosome condensation GO:0007076 The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. GOC:mah ISBN:0815316194 The mitotic cell cycle process involving ESCRTIII that results in reformation of the nuclear envelope after mitotic nuclear division. In organisms undergoing closed mitosis this involves resealing or 'repair' of the nuclear envelope in the nuclear bridge. https://github.com/geneontology/go-ontology/issues/19950 https://github.com/geneontology/go-ontology/issues/20636 nuclear envelope repair nuclear envelope resealing biological_process mitotic nuclear envelope reassembly GO:0007084 mitotic nuclear membrane reassembly GO:0007084 The mitotic cell cycle process involving ESCRTIII that results in reformation of the nuclear envelope after mitotic nuclear division. In organisms undergoing closed mitosis this involves resealing or 'repair' of the nuclear envelope in the nuclear bridge. PMID:26040712 PMID:28242692 PMID:32109380 PMID:32848252 Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process GO:0007088 regulation of mitotic nuclear division GO:0007088 Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Homologous chromosome pairing begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete. Wikipedia:Synapsis chromosomal synapsis synapsis biological_process chromosomal pairing GO:0007129 homologous chromosome pairing at meiosis GO:0007129 The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Homologous chromosome pairing begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete. GOC:mtg_cell_cycle PMID:22582262 PMID:23117617 PMID:31811152 chromosomal synapsis GOC:ascb_2009 GOC:dph GOC:tb chromosomal pairing GOC:ascb_2009 GOC:dph GOC:tb A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. male nuclear division biological_process male meiosis GO:0007140 male meiotic nuclear division GO:0007140 A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. GOC:dph GOC:mah GOC:vw The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. spermatid nuclear differentiation biological_process GO:0007289 See also the Cell Ontology term 'spermatid ; CL:0000018'. spermatid nucleus differentiation GO:0007289 The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. GOC:bf GOC:dph GOC:jl GOC:mah The change in shape of the spermatid nucleus from a spherical structure to an elongated organelle, during the latter part of spermatid differentiation. spermatid nuclear elongation biological_process GO:0007290 spermatid nucleus elongation GO:0007290 The change in shape of the spermatid nucleus from a spherical structure to an elongated organelle, during the latter part of spermatid differentiation. GOC:bf GOC:dph GOC:jl GOC:mah ISBN:0879694238 Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator GO:0007346 regulation of mitotic cell cycle GO:0007346 Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes. Wikipedia:Dosage_compensation biological_process GO:0007549 dosage compensation GO:0007549 Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes. GOC:ems PMID:11498577 PMID:35306885 Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule. Reactome:R-HSA-2468039 Reactome:R-HSA-2473152 Reactome:R-HSA-6790987 Reactome:R-HSA-9636560 molecular_function GO:0008080 N-acetyltransferase activity GO:0008080 Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule. GOC:ai Reactome:R-HSA-2468039 Acetylation of SMC3 subunit of chromosomal arm associated cohesin by ESCO1 or ESCO2 Reactome:R-HSA-2473152 Acetylation of SMC3 subunit of centromeric chromatin associated cohesin by ESCO1 or ESCO2 Reactome:R-HSA-6790987 NAT10 acetylates cytidine-1337 and cytidine-1842 of 18S rRNA yielding 4-acetylcytidine-1377 and 4-acetylcytidine-1842 Reactome:R-HSA-9636560 Eis acetylates DUSP16 Catalytic activity that acts to modify DNA, driven by ATP hydrolysis. https://github.com/geneontology/go-ontology/issues/20876 https://github.com/geneontology/go-ontology/issues/21612 https://github.com/geneontology/go-ontology/issues/21775 GO:0004011 ATPase activity, acting on DNA ATPase, acting on DNA DNA dependent ATPase activity DNA-dependent ATPase activity DNA-dependent adenosinetriphosphatase activity adenosinetriphosphatase (DNA-dependent) molecular_function GO:0008094 ATP-dependent activity, acting on DNA GO:0008094 Catalytic activity that acts to modify DNA, driven by ATP hydrolysis. GOC:pdt Any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/23112 GO:0008105 GO:0016249 GO:0034613 cellular protein localisation cellular protein localization protein localisation channel localizer activity biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization GO:0008104 Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai cellular protein localisation GOC:mah protein localisation GOC:mah channel localizer activity GOC:mah asymmetric protein localisation GOC:mah Binding to a transcription factor, a protein required to initiate or regulate transcription. https://github.com/geneontology/go-ontology/issues/19354 TF binding molecular_function transcription regulator binding GO:0008134 Note that this term should not be used for direct annotation. Please consier one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding. transcription factor binding GO:0008134 Binding to a transcription factor, a protein required to initiate or regulate transcription. ISBN:0198506732 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process GO:0008150 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process GO:0008152 The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0004480 methylase EC:2.1.1.- Reactome:R-HSA-212269 Reactome:R-HSA-379387 Reactome:R-HSA-379464 Reactome:R-HSA-6800149 Reactome:R-HSA-71286 Reactome:R-HSA-9710490 molecular_function GO:0008168 methyltransferase activity GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. ISBN:0198506732 Reactome:R-HSA-212269 DNMT1,3A,3B:PRC2 methylates cytosine and histone H3 Reactome:R-HSA-379387 COMT transfers Met to DA to form 3MT Reactome:R-HSA-379464 COMT transfers Met to DOPAC to form HVA Reactome:R-HSA-6800149 N6AMT1:TRMT112 transfers CH3 group from AdoMet to MMAIII Reactome:R-HSA-71286 guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine Reactome:R-HSA-9710490 The GSDME gene promoter is hypermethylated Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule. EC:2.1.1.- molecular_function GO:0008170 N-methyltransferase activity GO:0008170 Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule. GOC:ai The addition of an alkyl group to a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom. protein amino acid alkylation biological_process GO:0008213 protein alkylation GO:0008213 The addition of an alkyl group to a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom. GOC:ma protein amino acid alkylation GOC:bf The removal of an alkyl group from a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom. protein amino acid dealkylation biological_process GO:0008214 protein dealkylation GO:0008214 The removal of an alkyl group from a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom. GOC:ai protein amino acid dealkylation GOC:bf Catalysis of the transfer of a methyl group (CH3-) to a protein. Reactome:R-HSA-9632182 protein methylase activity molecular_function GO:0008276 protein methyltransferase activity GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein. GOC:jl Reactome:R-HSA-9632182 PRMT1 methylates ESRs Binding to a methylated cytosine/guanine dinucleotide. molecular_function GO:0008327 methyl-CpG binding GO:0008327 Binding to a methylated cytosine/guanine dinucleotide. GOC:jl PMID:11746232 Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine. GO:0016276 Reactome:R-HSA-5205799 Reactome:R-HSA-5205861 Reactome:R-HSA-5216234 Reactome:R-HSA-5661117 Reactome:R-HSA-8936584 Reactome:R-HSA-8936608 Reactome:R-HSA-8937022 Reactome:R-HSA-8937113 S-adenosyl-L-methionine:histone-arginine nomega-methyltransferase activity S-adenosyl-L-methionine:histone-arginine omega-N-methyltransferase activity histone-arginine N-methylase activity histone-arginine N-methyltransferase activity molecular_function GO:0008469 histone arginine N-methyltransferase activity GO:0008469 Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine. PMID:8002954 Reactome:R-HSA-5205799 CCND1:CDK4:PRMT5:pT5-WDR77 methylates arginine-9 of histone H3 (H3R8) Reactome:R-HSA-5205861 COPRS:CCND1:CDK4:PRMT5:pT5-WDR77 methylates arginine-4 of histone H4 (H4R3) Reactome:R-HSA-5216234 PRMT5:pT5-WDR77 methylates arginine-4 of histone H2A (H2AR3) Reactome:R-HSA-5661117 CCND1:CDK4:PRMT5:pT5-WDR77 methylates methyl-arginine-9 of histone H3 Reactome:R-HSA-8936584 PRMT6 arginine methylates H3K4me2-Nucleosome at the ITGA2B gene promoter Reactome:R-HSA-8936608 PRMT6 arginine methylates H3K4me2-Nucleosome at the GP1BA gene promoter Reactome:R-HSA-8937022 PRMT6 arginine methylates H3K4me2-Nucleosome at the THBS1 gene promoter Reactome:R-HSA-8937113 PRMT6 arginine methylates H3K4me2-Nucleosome at the MIR27A gene promoter histone-arginine N-methylase activity GOC:mah Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate. S-adenosyl methionine-dependent methyltransferase activity SAM-dependent methyltransferase activity molecular_function GO:0008757 S-adenosylmethionine-dependent methyltransferase activity GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate. GOC:mah Catalysis of the transfer of a methyl group to a DNA molecule. DNA methylase Reactome:R-HSA-5227490 DNA methyltransferase activity DNA transmethylase activity deoxyribonucleate methylase activity deoxyribonucleate methyltransferase activity deoxyribonucleic acid methylase activity deoxyribonucleic acid methyltransferase activity molecular_function Type II DNA methylase deoxyribonucleic acid modification methylase activity GO:0009008 DNA-methyltransferase activity GO:0009008 Catalysis of the transfer of a methyl group to a DNA molecule. GOC:jl ISBN:0198506732 PMID:7862522 Reactome:R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes Type II DNA methylase EC:2.1.1.37 Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex. chromosome inactivation Wikipedia:X-inactivation X chromosome inactivation biological_process Barr body formation GO:0009048 dosage compensation by inactivation of X chromosome GO:0009048 Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex. GOC:jl GOC:mr GOC:pr ISBN:0140512888 PMID:11498577 PMID:20622855 Wikipedia:XY_sex-determination_system Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process GO:0009889 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process GO:0009890 Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process GO:0009891 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process GO:0009892 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process GO:0009893 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process GO:0009987 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Compaction of chromatin structure prior to meiosis in eukaryotic cells. chromosome condensation involved in meiotic cell cycle biological_process GO:0010032 meiotic chromosome condensation GO:0010032 Compaction of chromatin structure prior to meiosis in eukaryotic cells. PMID:10072401 chromosome condensation involved in meiotic cell cycle GOC:dph GOC:tb The modification of histones by addition of a single ubiquitin group. biological_process GO:0010390 histone monoubiquitination GO:0010390 The modification of histones by addition of a single ubiquitin group. PMID:17329563 The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule. cytosine methylation within a CG sequence biological_process GO:0010424 DNA methylation on cytosine within a CG sequence GO:0010424 The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule. GOC:dph GOC:tb PMID:17239600 cytosine methylation within a CG sequence GOC:dph GOC:tb The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone. histone H3 K36 methylation histone H3K36me histone lysine H3 K36 methylation biological_process GO:0010452 histone H3-K36 methylation GO:0010452 The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone. GOC:pr GOC:tb histone H3 K36 methylation GOC:tb histone H3K36me GOC:tb histone lysine H3 K36 methylation GOC:tb Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process gene regulation regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression GO:0010468 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 gene regulation GOC:cjm Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3. H3 histone acetylase activity H3 histone acetyltransferase activity molecular_function GO:0010484 histone H3 acetyltransferase activity GO:0010484 Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3. EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H4 = CoA + acetyl-histone H4. H4 histone acetylase activity H4 histone acetyltransferase activity molecular_function GO:0010485 histone H4 acetyltransferase activity GO:0010485 Catalysis of the reaction: acetyl-CoA + histone H4 = CoA + acetyl-histone H4. EC:2.3.1.48 Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process GO:0010556 Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process GO:0010557 Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process GO:0010558 Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process GO:0010564 regulation of cell cycle process GO:0010564 Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle. positive regulation of DNA replication involved in S phase positive regulation of DNA replication involved in S-phase biological_process positive regulation of DNA replication during S phase GO:0010571 positive regulation of nuclear cell cycle DNA replication GO:0010571 Any process that activates or increases the frequency, rate or extent of the DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle. GOC:mtg_cell_cycle positive regulation of DNA replication during S phase GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010604 positive regulation of macromolecule metabolic process GO:0010604 Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010605 negative regulation of macromolecule metabolic process GO:0010605 Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process GO:0010628 positive regulation of gene expression GO:0010628 Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process gene silencing GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression GO:0010629 Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization GO:0010638 Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative regulation of organelle organization GO:0010639 Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of mRNA from the nucleus to the cytoplasm. biological_process GO:0010793 regulation of mRNA export from nucleus GO:0010793 Any process that modulates the frequency, rate or extent of the directed movement of mRNA from the nucleus to the cytoplasm. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-04-27T09:53:22Z biological_process GO:0010948 negative regulation of cell cycle process GO:0010948 Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane integral to membrane membrane region region of membrane whole membrane cellular_component transmembrane GO:0016020 membrane GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 transmembrane GOC:mah A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization GO:0016043 A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers. NIF_Subcellular:sao120573470 Wikipedia:Inclusion_bodies neuronal cytoplasmic inclusion cellular_component cellular inclusion GO:0016234 inclusion body GO:0016234 A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers. GOC:mah PMID:11121744 cellular inclusion NIF_Subcellular:sao120573470 Enables the transfer of a methyl group from S-adenosyl-L-methionine to an amino group of an arginine residue. molecular_function GO:0016273 arginine N-methyltransferase activity GO:0016273 Enables the transfer of a methyl group from S-adenosyl-L-methionine to an amino group of an arginine residue. GOC:mah Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine. Reactome:R-HSA-191790 Reactome:R-HSA-5205798 Reactome:R-HSA-5205820 Reactome:R-HSA-5205822 Reactome:R-HSA-5205824 Reactome:R-HSA-5205867 Reactome:R-HSA-5218952 Reactome:R-HSA-5229010 Reactome:R-HSA-5229203 Reactome:R-HSA-5661126 Reactome:R-HSA-8879123 Reactome:R-HSA-8934735 PRMT activity molecular_function GO:0016274 protein-arginine N-methyltransferase activity GO:0016274 Reactome:R-HSA-5205822 CARM1 methylates arginine-18 (H3R17) of histone H3 Reactome:R-HSA-5205824 CARM1, PRMT6 methylate arginine-3 of histone H3 (H3R2) Reactome:R-HSA-5205867 PRMT1 methylates arginine-12 of histone H2A (H2AR11) Reactome:R-HSA-5218952 PRMT5:WDR77, PRMT7 methylate arginine-3 of histone H3 (H3R2) Reactome:R-HSA-5229010 CARM1 methylates arginine-27 of histone H3 (H3R26) Reactome:R-HSA-5229203 PRMT6 methylates histone H2A arginine-30 (H2AR29) Reactome:R-HSA-5661126 PRMT1,PRMT6 methylate methyl-lysine-4 of histone H4 Reactome:R-HSA-8879123 PRMT3 transfers 3xCH3 from 3xAdoMet to RPS2 Reactome:R-HSA-8934735 PRMT1 arginine-methylates RUNX1 Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine. GOC:mah PMID:12351636 PMID:31284549 Reactome:R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes Reactome:R-HSA-5205798 PRMT1,PRMT6 methylate arginine-4 of histone H4 Reactome:R-HSA-5205820 PRMT6 methylates arginine-4 of histone H2A (H2AR3) Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue. Reactome:R-HSA-3222237 Reactome:R-HSA-6805730 Reactome:R-HSA-6805740 Reactome:R-HSA-6805755 molecular_function GO:0016278 lysine N-methyltransferase activity GO:0016278 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue. GOC:mah Reactome:R-HSA-3222237 SMYD2 methylates TP53 Reactome:R-HSA-6805730 SETD9 methylates TP53 Reactome:R-HSA-6805740 SETD8 methylates TP53 Reactome:R-HSA-6805755 EHMT1:EHMT2 dimethylates TP53 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate. RHEA:51736 Reactome:R-HSA-212263 Reactome:R-HSA-8865237 Reactome:R-HSA-8931858 Reactome:R-HSA-8931974 Reactome:R-HSA-8932221 Reactome:R-HSA-8932243 Reactome:R-HSA-8932275 Reactome:R-HSA-8932276 Reactome:R-HSA-8932413 protein (lysine) methyltransferase activity protein lysine methylase activity molecular_function GO:0016279 protein-lysine N-methyltransferase activity GO:0016279 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate. PMID:12054878 Reactome:R-HSA-212263 PRC2 trimethylates histone H3 at lysine-27 Reactome:R-HSA-8865237 SETD6 methylates RELA in the NFkB complex Reactome:R-HSA-8931858 ETFBKMT transfers 3xCH3 from 3xAdoMet to ETFB Reactome:R-HSA-8931974 N6AMT2 transfers 3xCH3 from 3xAdoMet to EEF1A Reactome:R-HSA-8932221 METTL21A transfers 3xCH3 from 3xAdoMet to HSPA8 Reactome:R-HSA-8932243 EEF2KMT transfers 3xCH3 from 3xAdoMet to EEF2 Reactome:R-HSA-8932275 METTL22 transfers 3xCH3 from 3xAdoMet to KIN Reactome:R-HSA-8932276 VCPKMT (METTL21D) transfers 3xCH3 from 3xAdoMet to VCP Reactome:R-HSA-8932413 METTL10 transfers 3xCH3 from 3xAdoMet to EEF1A1 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The dense fibrillar network lying on the inner side of the nuclear membrane. Wikipedia:Nuclear_matrix nucleoskeleton cellular_component GO:0016363 nuclear matrix GO:0016363 The dense fibrillar network lying on the inner side of the nuclear membrane. ISBN:0582227089 Catalysis of the transfer of an acetyl group to an acceptor molecule. Reactome:R-HSA-5628871 Reactome:R-HSA-5660660 Reactome:R-HSA-5682044 Reactome:R-HSA-6792712 Reactome:R-HSA-6805638 Reactome:R-HSA-73736 acetylase activity molecular_function GO:0016407 acetyltransferase activity GO:0016407 Catalysis of the transfer of an acetyl group to an acceptor molecule. GOC:ai Reactome:R-HSA-5628871 BRD7 promotes EP300-mediated acetylation of TP53 Reactome:R-HSA-5660660 p300 acetylates RELA subunit Reactome:R-HSA-5682044 KAT5 acetylates ATM at DNA DSBs Reactome:R-HSA-6792712 KAT5 acetylates ATM at shortened telomeres Reactome:R-HSA-6805638 KAT6A acetylates TP53 Reactome:R-HSA-73736 Acetylation of SL1 Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule. Reactome:R-HSA-177160 molecular_function GO:0016410 N-acyltransferase activity GO:0016410 Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule. GOC:ai Reactome:R-HSA-177160 phenylacetyl-CoA + glutamine => phenylacetyl glutamine + Coenzyme A Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. EC:1.-.-.- Reactome:R-HSA-1614362 Reactome:R-HSA-209921 Reactome:R-HSA-209960 Reactome:R-HSA-3095889 Reactome:R-HSA-390425 Reactome:R-HSA-390438 Reactome:R-HSA-5662660 Reactome:R-HSA-8878581 Reactome:R-HSA-8936442 Reactome:R-HSA-9020249 Reactome:R-HSA-9020260 Reactome:R-HSA-9024624 Reactome:R-HSA-9024630 Reactome:R-HSA-9025007 Reactome:R-HSA-9026001 Reactome:R-HSA-9026917 Reactome:R-HSA-9027033 Reactome:R-HSA-9693722 redox activity oxidoreductase activity, acting on other substrates molecular_function GO:0016491 oxidoreductase activity GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GOC:go_curators Reactome:R-HSA-1614362 SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases Reactome:R-HSA-209921 Monoiodinated tyrosine can be deiodinated Reactome:R-HSA-209960 Diiodinated tyrosine can be deiodinated Reactome:R-HSA-3095889 MMACHC dealkylates RCbl Reactome:R-HSA-390425 FAR1 reduces PalmCoA to HXOL Reactome:R-HSA-390438 FAR2 reduces PalmCoA to HXOL Reactome:R-HSA-5662660 Dopachrome is transformed to DHICA by DCT Reactome:R-HSA-8878581 TYRP1 oxidises DHICA to IQCA Reactome:R-HSA-8936442 MARC1,MARC2 reduce N-hydroxylated compounds Reactome:R-HSA-9020249 Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6 Reactome:R-HSA-9020260 Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5 Reactome:R-HSA-9024624 Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6 Reactome:R-HSA-9024630 Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5 Reactome:R-HSA-9025007 Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1 Reactome:R-HSA-9026001 Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA Reactome:R-HSA-9026917 Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA Reactome:R-HSA-9027033 Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA Reactome:R-HSA-9693722 Unknown sepiapterin synthase transforms PTHP to sepiapterin A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the yeast SNF2 or mammalian SMARCA4/BAF190A/BRG1 gene, or an ortholog thereof. SWI-SNF complex cellular_component GO:0016514 SWI/SNF complex GO:0016514 A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the yeast SNF2 or mammalian SMARCA4/BAF190A/BRG1 gene, or an ortholog thereof. GOC:bhm PMID:12672490 SWI-SNF complex GOC:mah The process in which one or more ubiquitin groups are added to a protein. protein ubiquitinylation protein ubiquitylation biological_process GO:0016567 protein ubiquitination GO:0016567 The process in which one or more ubiquitin groups are added to a protein. GOC:ai The covalent alteration of one or more amino acid residues within a histone protein. Wikipedia:Histone#Histone_modifications_in_chromatin_regulation biological_process GO:0016570 histone modification GO:0016570 The covalent alteration of one or more amino acid residues within a histone protein. GOC:krc The modification of histones by addition of methyl groups. Wikipedia:Histone_methylation biological_process GO:0016571 histone methylation GO:0016571 The modification of histones by addition of methyl groups. GOC:ai The modification of a histone by the addition of an acetyl group. biological_process GO:0016573 histone acetylation GO:0016573 The modification of a histone by the addition of an acetyl group. GOC:ai The modification of histones by addition of ubiquitin groups. histone ubiquitinylation histone ubiquitylation biological_process GO:0016574 histone ubiquitination GO:0016574 The modification of histones by addition of ubiquitin groups. GOC:ai The modification of histones by removal of acetyl groups. biological_process GO:0016575 histone deacetylation GO:0016575 The modification of histones by removal of acetyl groups. GOC:ai The modification of histones by removal of methyl groups. biological_process GO:0016577 histone demethylation GO:0016577 The modification of histones by removal of methyl groups. GOC:ai The modification of histones by removal of ubiquitin groups. histone deubiquitinylation histone deubiquitylation biological_process GO:0016578 histone deubiquitination GO:0016578 The modification of histones by removal of ubiquitin groups. GOC:ai The removal of one or more ubiquitin groups from a protein. GO:0006514 deubiquitination protein deubiquitinylation protein deubiquitylation biological_process GO:0016579 protein deubiquitination GO:0016579 The removal of one or more ubiquitin groups from a protein. GOC:ai A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins. cellular_component GO:0016580 Sin3 complex GO:0016580 A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins. PMID:10589671 PMID:11743021 PMID:12865422 An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins. https://github.com/geneontology/go-ontology/issues/23685 NRD complex nucleosome remodeling and histone deacetylation complex Mi-2 complex cellular_component GO:0016581 NuRD complex GO:0016581 An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins. PMID:10589671 PMID:11743021 PMID:17289569 An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters. nucleosome remodeling factor complex cellular_component GO:0016589 NURF complex GO:0016589 An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters. GOC:bf GOC:krc PMID:10779516 PMID:11279013 PMID:15284901 PMID:16568949 PMID:21810179 An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and generally no other subunits, though Xenopus is an exception with a third non-conserved subunit. ACF plays roles in regulation of RNA polymerase II transcription and in DNA replication and repair. ATP-utilizing chromatin assembly and remodeling factor complex cellular_component GO:0016590 ACF complex GO:0016590 An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and generally no other subunits, though Xenopus is an exception with a third non-conserved subunit. ACF plays roles in regulation of RNA polymerase II transcription and in DNA replication and repair. GOC:bf GOC:krc PMID:12192034 PMID:15284901 PMID:16568949 PMID:21810179 A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae. cellular_component GO:0016600 See also the cellular component term 'caveola ; GO:0005901'. flotillin complex GO:0016600 A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae. PMID:17206938 PMID:17600709 A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5. cellular_component CBF complex NF-Y transcription factor complex nuclear transcription factor Y complex GO:0016602 CCAAT-binding factor complex GO:0016602 A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5. GOC:bhm PMID:7828851 CBF complex GOC:bhm NF-Y transcription factor complex GOC:bhm nuclear transcription factor Y complex GOC:bhm Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. NIF_Subcellular:sao505137457 cellular_component GO:0016604 nuclear body GO:0016604 Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins. GOC:ma PMID:10330182 A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. nuclear speckle nuclear speckles splicing speckle speckle domain cellular_component speckle focus GO:0016607 nuclear speck GO:0016607 A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. http://www.cellnucleus.com/ Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. EC:1.14.-.- oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, miscellaneous molecular_function GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. GOC:mah Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor. GO:0010302 EC:1.14.11.- Reactome:R-HSA-1234164 Reactome:R-HSA-6783455 2-oxoglutarate dioxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors molecular_function GO:0016706 2-oxoglutarate-dependent dioxygenase activity GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor. GOC:mah Reactome:R-HSA-1234164 Cytosolic HIF1AN (FIH1) hydroxylates asparagine residues of Hypoxia-inducible Factor Alpha (HIF1A,HIF2A) Reactome:R-HSA-6783455 TYW5 hydroxylates yW-72 yielding OHyW-72 at nucleotide 37 of tRNA(Phe) Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor). https://github.com/geneontology/go-ontology/issues/20486 EC:2.1.-.- methyltransferase activity molecular_function GO:0016741 transferase activity, transferring one-carbon groups GO:0016741 Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). https://github.com/geneontology/go-ontology/issues/20486 GO:0008415 EC:2.3.-.- Reactome:R-HSA-159431 Reactome:R-HSA-192312 Reactome:R-HSA-193491 Reactome:R-HSA-6792572 Reactome:R-HSA-8858298 transferase activity, transferring acyl groups molecular_function GO:0016746 acyltransferase activity GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Reactome:R-HSA-159431 Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine Reactome:R-HSA-192312 Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate Reactome:R-HSA-193491 Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate Reactome:R-HSA-6792572 LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs Reactome:R-HSA-8858298 HRASLS transfer acyl group from PC to PE to form NAPE Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor). https://github.com/geneontology/go-ontology/issues/20486 EC:2.3.1.- transferase activity, transferring acyl groups other than amino-acyl groups molecular_function transferase activity, transferring groups other than amino-acyl groups GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor). GOC:jl transferase activity, transferring groups other than amino-acyl groups EC:2.3.1.- Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7.-.- molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups GO:0016772 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). EC:2.7.1.- Reactome:R-HSA-2161193 molecular_function GO:0016773 phosphotransferase activity, alcohol group as acceptor GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). GOC:jl Reactome:R-HSA-2161193 abacavir + AMP => abacavir monophosphate + adenosine Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. EC:3.-.-.- Reactome:R-HSA-1236938 Reactome:R-HSA-2029475 Reactome:R-HSA-5694583 Reactome:R-HSA-5695964 Reactome:R-HSA-6786190 Reactome:R-HSA-6788295 Reactome:R-HSA-8938314 Reactome:R-HSA-8952137 molecular_function GO:0016787 hydrolase activity GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. ISBN:0198506732 Reactome:R-HSA-1236938 Partial proteolysis of antigen in phagolysosomes Reactome:R-HSA-2029475 Production of AA by iPLA2 upon FCGR activation Reactome:R-HSA-5694583 ABHD4 hydrolyses NAPE Reactome:R-HSA-5695964 ABHD14B hydrolyses PNPB Reactome:R-HSA-6786190 CMBL hydrolyses OM to OLMS Reactome:R-HSA-6788295 HDHD1:Mg2+ dephosphorylates PURIDP Reactome:R-HSA-8938314 ENPPs hydrolyse CoA-SH to PPANT, PAP Reactome:R-HSA-8952137 Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate Catalysis of the hydrolysis of any ester bond. EC:3.1.-.- Reactome:R-HSA-162729 Reactome:R-HSA-9023617 Reactome:R-HSA-9023619 Reactome:R-HSA-9749609 esterase activity molecular_function GO:0016788 hydrolase activity, acting on ester bonds GO:0016788 Catalysis of the hydrolysis of any ester bond. GOC:jl Reactome:R-HSA-162729 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid Reactome:R-HSA-9023617 Butyrylcholinesterase hydrolyzes acyl Ghrelin Reactome:R-HSA-9023619 Platelet-activating factor acetylhydrolase (PLA2G7) hydrolyzes acyl Ghrelin Reactome:R-HSA-9749609 BCHE hydrolyzes ASA- Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GO:0003869 GO:0016302 EC:3.1.3.- MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN Reactome:R-HSA-4419986 Reactome:R-HSA-9636457 phosphoric monoester hydrolase activity 4-nitrophenylphosphatase activity 4-nitrophenylphosphate phosphohydrolase activity K-pNPPase activity NPPase activity PNPPase activity ecto-p-nitrophenyl phosphatase activity nitrophenyl phosphatase activity p-nitrophenylphosphatase activity p-nitrophenylphosphate phosphohydrolase activity para-nitrophenyl phosphatase activity molecular_function phosphatase GO:0016791 phosphatase activity GO:0016791 Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate. GOC:curators GOC:pg Reactome:R-HSA-4419986 Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL Reactome:R-HSA-9636457 SapM dephosphorylates PI3P Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds. EC:3.5.-.- Reactome:R-HSA-6803753 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in other compounds molecular_function GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds. GOC:jl Reactome:R-HSA-6803753 NAAA hydrolyses NAEs to FAs and ethanolamine Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. EC:3.5.1.- Reactome:R-HSA-9673053 Reactome:R-HSA-9673054 molecular_function GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. GOC:ai Reactome:R-HSA-9673053 PM20D1 transforms oleoyl-phe from oleate and phe Reactome:R-HSA-9673054 PM20D1 hydrolyzes oleoyl-phe Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand. GO:0035257 GO:0035258 steroid hormone receptor binding ligand-dependent nuclear receptor binding nuclear hormone receptor binding molecular_function ligand-dependent nuclear receptor interactor activity GO:0016922 nuclear receptor binding GO:0016922 Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand. PMID:7776974 A complex consisting of two distinct motor subunits that form a heterodimer complexed with a third non-motor accessory subunit, the kinesin associated protein or KAP; the KIF3 heterodimer interacts via its C-terminal portion with KAP, which is thought to regulate the binding of the motor to cargo membranes. cellular_component GO:0016939 kinesin II complex GO:0016939 A complex consisting of two distinct motor subunits that form a heterodimer complexed with a third non-motor accessory subunit, the kinesin associated protein or KAP; the KIF3 heterodimer interacts via its C-terminal portion with KAP, which is thought to regulate the binding of the motor to cargo membranes. http://www.csfic.mi.cnr.it/centro/lines/8/ric.html Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone. molecular_function SIR2 GO:0017136 NAD-dependent histone deacetylase activity GO:0017136 Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone. PMID:28450737 The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative. biological_process GO:0018022 peptidyl-lysine methylation GO:0018022 The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative. GOC:ai The methylation of peptidyl-lysine to form peptidyl-N6,N6,N6-trimethyl-L-lysine. RESID:AA0074 biological_process GO:0018023 peptidyl-lysine trimethylation GO:0018023 The methylation of peptidyl-lysine to form peptidyl-N6,N6,N6-trimethyl-L-lysine. RESID:AA0074 The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine. RESID:AA0075 biological_process GO:0018027 peptidyl-lysine dimethylation GO:0018027 The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine. RESID:AA0075 The alteration of an amino acid residue in a peptide. biological_process GO:0018193 peptidyl-amino acid modification GO:0018193 The alteration of an amino acid residue in a peptide. GOC:mah The modification of peptidyl-arginine. biological_process GO:0018195 peptidyl-arginine modification GO:0018195 The modification of peptidyl-arginine. GOC:go_curators The modification of peptidyl-lysine. biological_process GO:0018205 peptidyl-lysine modification GO:0018205 The modification of peptidyl-lysine. GOC:go_curators The addition of a methyl group to an arginine residue in a protein. GO:0018017 biological_process GO:0018216 peptidyl-arginine methylation GO:0018216 The addition of a methyl group to an arginine residue in a protein. GOC:mah The modification of a protein by the addition of a succinyl group (CO-CH2-CH2-CO) to an amino acid residue. protein amino acid succinylation biological_process GO:0018335 protein succinylation GO:0018335 The modification of a protein by the addition of a succinyl group (CO-CH2-CH2-CO) to an amino acid residue. GOC:bf protein amino acid succinylation GOC:bf The addition of an acetyl group to a non-terminal lysine residue in a protein. biological_process GO:0018393 internal peptidyl-lysine acetylation GO:0018393 The addition of an acetyl group to a non-terminal lysine residue in a protein. GOC:mah The acetylation of peptidyl-lysine. biological_process GO:0018394 peptidyl-lysine acetylation GO:0018394 The acetylation of peptidyl-lysine. GOC:mah Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. Reactome:R-HSA-141367 Reactome:R-HSA-162914 GO:0019107 myristoyltransferase activity GO:0019107 Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. GOC:ai Reactome:R-HSA-141367 Myristoylation of tBID by NMT1 Reactome:R-HSA-162914 Myristoylation of Nef Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. Reactome:R-HSA-5689000 molecular_function GO:0019213 deacetylase activity GO:0019213 Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. GOC:jl Reactome:R-HSA-5689000 AADAC deacetylates PHEN Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process GO:0019219 Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process GO:0019222 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 GO:0006411 GO:0044267 GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism protein metabolic process and modification protein metabolism protein metabolism and modification multicellular organismal protein metabolic process biological_process GO:0019538 protein metabolic process GO:0019538 The chemical reactions and pathways involving a protein. Includes protein modification. GOC:ma A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. antibody cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex GO:0019814 A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add GOC:jl ISBN:0781765196 The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites. cellular_component GO:0019866 See also the cellular component term 'outer membrane ; GO:0019867'. organelle inner membrane GO:0019866 The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites. GOC:mah Binding to an enzyme, a protein with catalytic activity. molecular_function GO:0019899 enzyme binding GO:0019899 Binding to an enzyme, a protein with catalytic activity. GOC:jl The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process GO:0022402 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism GO:0022412 A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process GO:0022414 A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly GO:0022607 The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete Binds to and modulates the activity of an enzyme. GO:0010576 catalytic regulator activity enzyme modulator metalloenzyme regulator activity molecular_function GO:0030234 This term should only be used in cases when the regulator directly interacts with the enzyme. enzyme regulator activity GO:0030234 Binds to and modulates the activity of an enzyme. GOC:dph GOC:mah GOC:tb catalytic regulator activity GOC:dph The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation biological_process GO:0030261 chromosome condensation GO:0030261 The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:mah ISBN:0815316194 DNA condensation Wikipedia:DNA_condensation eukaryotic chromosome condensation GOC:bf nuclear chromosome condensation GOC:bf Binding to a nuclear estrogen receptor. https://github.com/geneontology/go-ontology/issues/16717 estrogen receptor binding molecular_function GO:0030331 nuclear estrogen receptor binding GO:0030331 Binding to a nuclear estrogen receptor. GOC:ai A transcription coactivator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator. https://github.com/geneontology/go-ontology/issues/20253 https://github.com/geneontology/go-ontology/issues/20464 bf 2011-11-29T01:53:30Z GO:0038049 ligand-activated RNA polymerase II transcription factor binding transcription factor activity ligand-dependent nuclear receptor transcription co-activator activity ligand-dependent nuclear receptor transcription coactivator activity nuclear receptor transcription coactivator activity transcription factor activity, ligand-activated RNA polymerase II transcription factor binding molecular_function GO:0030374 For usage guidance, see comment in GO:0003712 ; transcription coregulator activity. nuclear receptor coactivator activity GO:0030374 A transcription coactivator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator. GOC:dph GOC:tb A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs. Wikipedia:SnRNP small nuclear ribonucleoprotein snRNP cellular_component GO:0030532 small nuclear ribonucleoprotein complex GO:0030532 A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs. GOC:krc GOC:mah ISBN:0879695897 The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid. https://github.com/geneontology/go-ontology/issues/18655 https://github.com/geneontology/go-ontology/issues/19409 https://github.com/geneontology/go-ontology/issues/22925 protein binding, bridging protein-protein adaptor molecular_function protein recruiting activity GO:0030674 protein-macromolecule adaptor activity GO:0030674 The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid. GOC:bf GOC:mah GOC:vw Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins. MRN complex MRX complex RAD50-MRE11-NBN complex RMX complex Rad50 complex Rad50-Rad32-Nbs1 complex cellular_component GO:0030870 Mre11 complex GO:0030870 Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins. GOC:mah GOC:vw PMID:11988766 PMID:17674145 RAD50-MRE11-NBN complex CORUM:2767 The portion of nuclear chromatin associated with the nucleolus; includes the DNA encoding the ribosomal RNA. cellular_component GO:0030874 nucleolar chromatin GO:0030874 The portion of nuclear chromatin associated with the nucleolus; includes the DNA encoding the ribosomal RNA. GOC:mah Any nuclear protein complex that contains an ATPase subunit of the imitation switch (ISWI) family. ISWI ATPases are involved in assembling chromatin and in sliding and spacing nucleosomes to regulate transcription of nuclear RNA polymerases I, II, and III and also DNA replication, recombination and repair. cellular_component GO:0031010 ISWI-type complex GO:0031010 Any nuclear protein complex that contains an ATPase subunit of the imitation switch (ISWI) family. ISWI ATPases are involved in assembling chromatin and in sliding and spacing nucleosomes to regulate transcription of nuclear RNA polymerases I, II, and III and also DNA replication, recombination and repair. GOC:krc GOC:mah PMID:15020051 PMID:15284901 PMID:16568949 PMID:21810179 Any process that modulates the frequency, rate or extent of the covalent alteration of a histone. biological_process GO:0031056 regulation of histone modification GO:0031056 Any process that modulates the frequency, rate or extent of the covalent alteration of a histone. GOC:mah Any process that modulates the frequency, rate or extent of the covalent addition of methyl groups to histones. biological_process GO:0031060 regulation of histone methylation GO:0031060 Any process that modulates the frequency, rate or extent of the covalent addition of methyl groups to histones. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of methyl groups to histones. down regulation of histone methylation down-regulation of histone methylation downregulation of histone methylation inhibition of histone methylation biological_process GO:0031061 negative regulation of histone methylation GO:0031061 Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of methyl groups to histones. GOC:mah Any process that activates or increases the frequency, rate or extent of the covalent addition of methyl groups to histones. up regulation of histone methylation up-regulation of histone methylation upregulation of histone methylation activation of histone methylation stimulation of histone methylation biological_process GO:0031062 positive regulation of histone methylation GO:0031062 Any process that activates or increases the frequency, rate or extent of the covalent addition of methyl groups to histones. GOC:mah Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones. biological_process GO:0031063 regulation of histone deacetylation GO:0031063 Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones. GOC:mah Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones. up regulation of histone deacetylation up-regulation of histone deacetylation upregulation of histone deacetylation activation of histone deacetylation stimulation of histone deacetylation biological_process GO:0031065 positive regulation of histone deacetylation GO:0031065 Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones. GOC:mah Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein. histone H3-K14 deacetylase activity histone deacetylase activity (H3-K14 specific) molecular_function GO:0031078 histone H3K14 deacetylase activity GO:0031078 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein. PMID:28450737 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane GO:0031090 A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group to the lysine residue at position 79 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/24337 histone H3K79 methylase activity histone lysine N-methyltransferase activity (H3-K79 specific) histone methylase activity (H3-K79 specific) histone methyltransferase activity (H3-K79 specific) histone-H3K79 methyltransferase activity molecular_function GO:0031151 histone H3K79 methyltransferase activity GO:0031151 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group to the lysine residue at position 79 of the histone H3 protein. GOC:mah PMID:15371351 histone methylase activity (H3-K79 specific) GOC:mah An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals) and an RSF1 homolog. It mediates nucleosome deposition and generates regularly spaced nucleosome arrays. In mammals, RSF is involved in regulation of transcription from RNA polymerase II promoters). remodeling and spacing factor complex cellular_component GO:0031213 RSF complex GO:0031213 An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals) and an RSF1 homolog. It mediates nucleosome deposition and generates regularly spaced nucleosome arrays. In mammals, RSF is involved in regulation of transcription from RNA polymerase II promoters). GOC:krc PMID:12972596 PMID:15284901 PMID:16568949 PMID:21810179 A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule. cellular_component GO:0031248 protein acetyltransferase complex GO:0031248 A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule. GOC:bf Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process GO:0031323 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process GO:0031324 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process GO:0031325 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process GO:0031326 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process GO:0031327 negative regulation of cellular biosynthetic process GO:0031327 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process GO:0031328 positive regulation of cellular biosynthetic process GO:0031328 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins. cellular_component GO:0031332 RNAi effector complex GO:0031332 Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins. GOC:mah PMID:14704433 Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. biological_process GO:0031399 regulation of protein modification process GO:0031399 Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. down regulation of protein modification down-regulation of protein modification downregulation of protein modification inhibition of protein modification biological_process GO:0031400 negative regulation of protein modification process GO:0031400 Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. up regulation of protein modification up-regulation of protein modification upregulation of protein modification activation of protein modification stimulation of protein modification biological_process GO:0031401 positive regulation of protein modification process GO:0031401 Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein. GOC:mah GOC:tb Any process that modulates the frequency, rate, extent or location of heterochromatin formation. https://github.com/geneontology/go-ontology/issues/23553 regulation of heterochromatin assembly biological_process GO:0031445 regulation of heterochromatin formation GO:0031445 Any process that modulates the frequency, rate, extent or location of heterochromatin formation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin formation. https://github.com/geneontology/go-ontology/issues/23553 chromatin decompaction chromatin decondensation down regulation of heterochromatin formation down-regulation of heterochromatin formation downregulation of heterochromatin formation negative regulation of heterochromatin assembly inhibition of heterochromatin formation biological_process GO:0031452 negative regulation of heterochromatin formation GO:0031452 Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin formation. PMID:16855380 chromatin decondensation PMID:16855380 Any process that activates or increases the frequency, rate or extent of heterochromatin formation. https://github.com/geneontology/go-ontology/issues/23553 positive regulation of heterochromatin assembly up regulation of heterochromatin formation up-regulation of heterochromatin formation upregulation of heterochromatin formation activation of heterochromatin formation stimulation of heterochromatin formation biological_process GO:0031453 positive regulation of heterochromatin formation GO:0031453 Any process that activates or increases the frequency, rate or extent of heterochromatin formation. GOC:mah The reformation of the nuclear membranes following their breakdown in the context of a normal process. https://github.com/geneontology/go-ontology/issues/20636 biological_process nuclear envelope reassembly GO:0031468 nuclear membrane reassembly GO:0031468 The reformation of the nuclear membranes following their breakdown in the context of a normal process. GOC:mah Binding to DNA that is assembled into chromatin. molecular_function GO:0031490 chromatin DNA binding GO:0031490 Binding to DNA that is assembled into chromatin. GOC:mah An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation. https://github.com/geneontology/go-ontology/issues/18954 https://github.com/geneontology/go-ontology/issues/19112 https://github.com/geneontology/go-ontology/issues/22030 https://github.com/geneontology/go-ontology/issues/23553 GO:0006342 GO:0006343 GO:0016440 GO:0070869 GO:1904497 TGS heterochromatin maintenance chromatin silencing chromatin-mediated silencing establishment of heterochromatin architecture heterochromatin assembly establishment of heterochromatin architecture involved in chromatin silencing at centromere outer repeat region establishment of heterochromatin architecture involved in chromatin silencing at pericentric region heterochromatin assembly involved in chromatin silencing at centromere outer repeat region heterochromatin assembly involved in chromatin silencing at pericentric region heterochromatin formation involved in chromatin silencing at centromere outer repeat region heterochromatin formation involved in chromatin silencing at pericentric region biological_process establishment of chromatin silencing establishment of heterochromatic silencing heterochromatic silencing heterochromatin assembly involved in chromatin silencing heterochromatin formation involved in chromatin silencing transcriptional gene silencing GO:0031507 heterochromatin formation GO:0031507 An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation. PMID:25192661 PMID:33827924 establishment of heterochromatin architecture GOC:mah establishment of heterochromatin architecture involved in chromatin silencing at centromere outer repeat region GOC:TermGenie establishment of heterochromatin architecture involved in chromatin silencing at pericentric region GOC:TermGenie heterochromatin assembly involved in chromatin silencing at pericentric region GOC:TermGenie heterochromatin formation involved in chromatin silencing at centromere outer repeat region GOC:TermGenie heterochromatin formation involved in chromatin silencing at pericentric region GOC:TermGenie The compaction of chromatin located adjacent to the CENP-A rich centromere 'central core' and characterized by methylation of histone H3K9, into heterochromatin, resulting in the repression of transcription at pericentric DNA. https://github.com/geneontology/go-ontology/issues/18954 https://github.com/geneontology/go-ontology/issues/19112 https://github.com/geneontology/go-ontology/issues/23553 https://github.com/geneontology/go-ontology/issues/23752 https://github.com/geneontology/go-ontology/issues/24791 mah 2013-07-17T15:21:38Z GO:0030702 GO:1990141 centromere chromatin silencing centromeric heterochromatin biosynthesis centromeric heterochromatin formation centromeric silencing chromatin silencing at centromere heterochromatic silencing at centromere pericentric heterochromatin assembly chromatin silencing at centromere outer repeat region biological_process centric heterochromatin formation chromatin silencing at pericentric region GO:0031508 pericentric heterochromatin formation GO:0031508 The compaction of chromatin located adjacent to the CENP-A rich centromere 'central core' and characterized by methylation of histone H3K9, into heterochromatin, resulting in the repression of transcription at pericentric DNA. GOC:mah PMID:14612388 PMID:20206496 PMID:22729156 centromere chromatin silencing GOC:mah centromeric silencing GOC:vw chromatin silencing at pericentric region GOC:mah The compaction of chromatin into heterochromatin at the subtelomeric region. https://github.com/geneontology/go-ontology/issues/19188 https://github.com/geneontology/go-ontology/issues/19308 https://github.com/geneontology/go-ontology/issues/22027 https://github.com/geneontology/go-ontology/issues/23553 GO:0006348 GO:0035390 GO:0099114 Telomere Position Effect chromatin silencing at telomere heterochromatic silencing at telomere subtelomeric heterochromatin assembly subtelomeric silencing telomere chromatin silencing telomeric silencing biological_process chromatin silencing at subtelomere establishment of chromatin silencing at telomere heterochromatic silencing at subtelomere regulation of chromatin silencing at telomere regulation of subtelomeric heterochromatin assembly subtelomere chromatin silencing telomeric heterochromatin assembly telomeric heterochromatin formation GO:0031509 subtelomeric heterochromatin formation GO:0031509 The compaction of chromatin into heterochromatin at the subtelomeric region. GOC:mah PMID:10219245 PMID:26205977 Telomere Position Effect GOC:BHF GOC:BHF_telomere GOC:nc PMID:21847107 subtelomeric silencing GOC:mah telomere chromatin silencing GOC:mah telomeric silencing GOC:bf subtelomere chromatin silencing GOC:mah A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. Polycomb Group protein complex cellular_component GO:0031519 PcG protein complex GO:0031519 A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure. PMID:9372908 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane GO:0031965 Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope GO:0031967 A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope GO:0031975 A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein. histone H3-K9 deacetylase activity histone deacetylase activity (H3-K9 specific) molecular_function GO:0032129 histone H3K9 deacetylase activity GO:0032129 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein. PMID:28450737 Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GO:0032239 regulation of nucleobase-containing compound transport GO:0032239 Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb The process in which a methyl group is covalently attached to a molecule. Wikipedia:Methylation biological_process GO:0032259 methylation GO:0032259 The process in which a methyl group is covalently attached to a molecule. GOC:mah Any complex formed of proteins that act in mismatch repair. cellular_component GO:0032300 mismatch repair complex GO:0032300 Any complex formed of proteins that act in mismatch repair. GOC:mah A heterodimer involved in the recognition and repair of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MSH2 and MSH6. MMR complex MSH2/MSH6 complex cellular_component GO:0032301 MutSalpha complex GO:0032301 A heterodimer involved in the recognition and repair of base-base and small insertion/deletion mismatches. In human the complex consists of two subunits, MSH2 and MSH6. PMID:11005803 Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process GO:0032386 regulation of intracellular transport GO:0032386 Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process GO:0032387 negative regulation of intracellular transport GO:0032387 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process GO:0032388 positive regulation of intracellular transport GO:0032388 Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target protein. biological_process GO:0032446 protein modification by small protein conjugation GO:0032446 A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target protein. GOC:mah Catalysis of the removal of a methyl group from a substrate. molecular_function GO:0032451 demethylase activity GO:0032451 Catalysis of the removal of a methyl group from a substrate. GOC:mah Catalysis of the removal of a methyl group from a histone. Reactome:R-HSA-3214912 Reactome:R-HSA-4722133 Reactome:R-HSA-4724279 Reactome:R-HSA-4724284 Reactome:R-HSA-4754176 Reactome:R-HSA-4754181 Reactome:R-HSA-4754187 Reactome:R-HSA-5423117 Reactome:R-HSA-5625797 Reactome:R-HSA-5625848 Reactome:R-HSA-5625870 Reactome:R-HSA-5661114 Reactome:R-HSA-5661115 Reactome:R-HSA-5661116 Reactome:R-HSA-5661120 Reactome:R-HSA-5661121 Reactome:R-HSA-5661122 Reactome:R-HSA-5661123 Reactome:R-HSA-5661124 Reactome:R-HSA-5661125 molecular_function GO:0032452 histone demethylase activity GO:0032452 Catalysis of the removal of a methyl group from a histone. GOC:mah Reactome:R-HSA-3214912 KDM1A, KDM1B demethylate MeK5-histone H3 Reactome:R-HSA-4722133 KDM2A, KDM2B, KDM4A demethylate MeK37-histone H3 Reactome:R-HSA-4724279 KDM4A, KDM4B, KDM4C, KDM4D demethylate Me2K10-histone H3 Reactome:R-HSA-4724284 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate MeK10-histone H3 Reactome:R-HSA-4754176 JMJD6 demethylates MeR3-histone H3 Reactome:R-HSA-4754181 KDM5A-D demethylate Me2K5-histone H3 Reactome:R-HSA-4754187 KDM6A, KDM6B, KDM7A demethylate Me2K28-histone H3 Reactome:R-HSA-5423117 PHF8 demethylates MeK21-histone H4 Reactome:R-HSA-5625797 KDM4C demethylates Me3K-10-H3 associated with KLK2 and KLK3 promoters Reactome:R-HSA-5625848 KDM1A demethylates dimethylated H3K9 (Me2K-10-H3) at KLK2 and KLK3 promoters Reactome:R-HSA-5625870 KDM1A demethylates monomethylated H3K9 (MeK-10-H3) at KLK2 and KLK3 promoters Reactome:R-HSA-5661114 KDM2A, KDM2B, KDM4A demethylate Me2K37-histone H3 Reactome:R-HSA-5661115 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate Me2K10-histone H3 Reactome:R-HSA-5661116 KDM5A-D demethylate Me3K5-histone H3 Reactome:R-HSA-5661120 KDM4A, KDM4B, KDM4C, KDM4D, MINA demethylate Me3K10-histone H3 Reactome:R-HSA-5661121 KDM6A, KDM6B, KDM7A demethylate Me3K28-histone H3 Reactome:R-HSA-5661122 JMJD6 demethylates Me2R3-histone H3 Reactome:R-HSA-5661123 KDM1A, KDM1B demethylate Me2K5-histone H3 Reactome:R-HSA-5661124 JMJD6 demethylates MeR4-HIST1H4 Reactome:R-HSA-5661125 JMJD6 demethylates Me2sR4-HIST1H4 Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/21089 histone H3-K4 demethylase activity histone H3-methyl-lysine-4 demethylase activity histone demethylase activity (H3-K4 specific) histone demethylase activity (H3K4-specific) molecular_function GO:0032453 histone H3K4 demethylase activity GO:0032453 Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein. GOC:mah Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/21089 Reactome:R-HSA-9011949 Reactome:R-HSA-9011985 Reactome:R-HSA-997263 histone H3-K49 demethylase activity histone H3-methyl-lysine-9 demethylase activity histone demethylase activity (H3-K9 specific) molecular_function GO:0032454 histone H3K9 demethylase activity GO:0032454 Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein. PMID:16362057 Reactome:R-HSA-9011949 KDM4B demethylates H3K9me3 on estrogen-responsive target enhancers Reactome:R-HSA-9011985 KDM1A demethylates H3 on MYC and BCL genes in response to estrogen Reactome:R-HSA-997263 JMJD1C demethylates H3K9 mono- and di-methylation Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. biological_process maintenance of protein localization in cell GO:0032507 maintenance of protein location in cell GO:0032507 Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. GOC:isa_complete GOC:mah maintenance of protein localization in cell GOC:dph GOC:tb The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule. cytosine methylation biological_process GO:0032776 DNA methylation on cytosine GO:0032776 The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule. GOC:pf A heterotrimeric H4/H2A histone acetyltransferase complex with a substrate preference of chromatin over free histones. It contains a subset of the proteins found in the larger NuA4 histone acetyltransferase complex; for example, the S. cerevisiae complex contains Esa1p, Yng2p, and Epl1p. cellular_component GO:0032777 Piccolo NuA4 histone acetyltransferase complex GO:0032777 A heterotrimeric H4/H2A histone acetyltransferase complex with a substrate preference of chromatin over free histones. It contains a subset of the proteins found in the larger NuA4 histone acetyltransferase complex; for example, the S. cerevisiae complex contains Esa1p, Yng2p, and Epl1p. GOC:rb PMID:12782659 PMID:15964809 A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus. SMN core complex survival motor neuron complex cellular_component GO:0032797 Note that a larger complex containing Sm proteins and other subunits is also sometimes referred to as the 'SMN complex'. The larger complex is represented by 'SMN-Sm protein complex ; GO:0034719'. SMN complex GO:0032797 A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus. PMID:16434402 PMID:17023415 Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization GO:0032879 Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:14Z GO:1903827 regulation of cellular protein localisation regulation of cellular protein localization regulation of protein localisation biological_process GO:0032880 regulation of protein localization GO:0032880 Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of cellular protein localisation GOC:TermGenie regulation of protein localisation GOC:mah A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex GO:0032991 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GOC:dos GOC:mah A macromolecular complex containing both protein and DNA molecules. DNA-protein complex cellular_component GO:0032993 Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. protein-DNA complex GO:0032993 A macromolecular complex containing both protein and DNA molecules. GOC:mah DNA-protein complex GOC:mah Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization GO:0033036 Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization GO:0033043 Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. regulation of chromosome organisation biological_process regulation of chromosome organization and biogenesis GO:0033044 regulation of chromosome organization GO:0033044 Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah Binding to a nuclear progesterone receptor. https://github.com/geneontology/go-ontology/issues/16717 progesterone receptor binding molecular_function GO:0033142 nuclear progesterone receptor binding GO:0033142 Binding to a nuclear progesterone receptor. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process GO:0033157 regulation of intracellular protein transport GO:0033157 Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. biological_process GO:0033169 histone H3-K9 demethylation GO:0033169 The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. GOC:mah Any process that modulates the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle. regulation of DNA replication involved in S phase regulation of DNA replication involved in S-phase biological_process regulation of DNA replication during S phase GO:0033262 regulation of nuclear cell cycle DNA replication GO:0033262 Any process that modulates the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle. GOC:mtg_cell_cycle regulation of DNA replication during S phase GOC:dph GOC:tb A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity. cellular_component GO:0033276 transcription factor TFTC complex GO:0033276 A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity. PMID:10373431 PMID:9603525 A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process GO:0033365 protein localization to organelle GO:0033365 A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah A region of heterochromatin located at the rDNA repeats in a chromosome. GO:1902377 ribosomal DNA heterochromatin nuclear rDNA heterochromatin ribosomal DNA heterochromatin of cell nucleus ribosomal DNA heterochromatin of nucleus cellular_component GO:0033553 rDNA heterochromatin GO:0033553 A region of heterochromatin located at the rDNA repeats in a chromosome. GOC:mah PMID:20661445 ribosomal DNA heterochromatin of cell nucleus GOC:TermGenie ribosomal DNA heterochromatin of nucleus GOC:TermGenie Catalysis of the reaction: H2O + N6-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein]. https://github.com/geneontology/go-ontology/issues/22833 RHEA:58108 Reactome:R-HSA-5693092 Reactome:R-HSA-8952069 Reactome:R-HSA-9626962 Reactome:R-HSA-9701565 protein deacetylase activity molecular_function GO:0033558 protein lysine deacetylase activity GO:0033558 Catalysis of the reaction: H2O + N6-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein]. PMID:27296530 RHEA:58108 Reactome:R-HSA-5693092 Unknown deacetylase deacetylates 7K-BACE1(46-501) Reactome:R-HSA-8952069 HDAC4 deacetylates RUNX3 Reactome:R-HSA-9626962 SIRT1 deacetylates FOXO1 Reactome:R-HSA-9701565 HDACs deacetylate p-STAT3 dimers true Catalysis of the removal of the methyl group from a modified arginine residue at position 2 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 histone H3-R2 demethylase activity histone H3-methyl-arginine-2 demethylase activity histone H3R2me demethylase activity histone demethylase activity (H3-R2 specific) molecular_function GO:0033746 histone H3R2 demethylase activity GO:0033746 Catalysis of the removal of the methyl group from a modified arginine residue at position 2 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:17947579 PMID:22483719 PMID:29233856 Catalysis of the removal of the methyl group from a modified arginine residue at position 3 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 https://github.com/geneontology/go-ontology/issues/24868 histone H4-methyl-arginine-3 demethylase activity histone H4R3me demethylase activity histone demethylase activity (H4-R3 specific) molecular_function GO:0033749 histone H4R3 demethylase activity GO:0033749 Catalysis of the removal of the methyl group from a modified arginine residue at position 3 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:17947579 Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide. Reactome:R-HSA-3371554 Reactome:R-HSA-9760081 molecular_function GO:0034212 peptide N-acetyltransferase activity GO:0034212 Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide. GOC:mah Reactome:R-HSA-3371554 HSF1 acetylation at Lys80 Reactome:R-HSA-9760081 CREBBP, EP300 acetylates NFE2L2 The portion of the nuclear lumen proximal to the inner nuclear membrane. cellular_component GO:0034399 nuclear periphery GO:0034399 The portion of the nuclear lumen proximal to the inner nuclear membrane. GOC:krc GOC:mah Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. protein localisation to chromosome condensin localization to chromosome biological_process GO:0034502 protein localization to chromosome GO:0034502 Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. GOC:mah protein localisation to chromosome GOC:mah A process in which a protein transports or maintains the localization of another protein to the nucleus. 2012-11-07T15:45:54Z GO:0044744 protein localisation to nucleus protein localization in cell nucleus protein localization in nucleus biological_process protein targeting to nucleus GO:0034504 protein localization to nucleus GO:0034504 A process in which a protein transports or maintains the localization of another protein to the nucleus. GOC:ecd protein localisation to nucleus GOC:mah protein localization in nucleus GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process GO:0034641 The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 histone H3-K4me2 demethylase activity histone H3K4me2 demethylase activity EC:1.14.11.67 RHEA:60208 histone H3-tri/di/monomethyl-lysine-4 demethylase activity histone demethylase activity (H3-K4-me3 specific) histone demethylase activity (H3-trimethyl-K4 specific) molecular_function H3K4me3 demethylase activity histone H3-K4me3 demethylase activity GO:0034647 histone H3K4me/H3K4me2/H3K4me3 demethylase activity GO:0034647 Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:17550896 PMID:22473470 A protein complex that possesses methyltransferase activity. cellular_component GO:0034708 methyltransferase complex GO:0034708 A protein complex that possesses methyltransferase activity. GOC:mah A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm. SMN-containing protein complex cellular_component GO:0034719 Note that this complex is sometimes referred to as the 'SMN complex', but it should not be confused with GO:0032797. SMN-Sm protein complex GO:0034719 A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm. GOC:vw PMID:11522829 PMID:17401408 The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone. biological_process H3K4 demethylation (me1 me2 and me3) GO:0034720 histone H3-K4 demethylation GO:0034720 The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone. GOC:mah The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone. histone H3 K79 methylation histone H3K79me histone lysine H3 K79 methylation biological_process GO:0034729 histone H3-K79 methylation GO:0034729 The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone. GOC:se Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein. histone H4-K16 deacetylase activity histone deacetylase activity (H4-K16 specific) molecular_function GO:0034739 histone H4K16 deacetylase activity GO:0034739 Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein. GOC:vw PMID:28450737 The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone. histone H4 K20 methylation histone H4K20me histone lysine H4 K20 methylation biological_process GO:0034770 histone H4-K20 methylation GO:0034770 The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone. GOC:mah The modification of histone H4 by addition of two methyl groups to lysine at position 20 of the histone. histone H4 K20 dimethylation histone lysine H4 K20 dimethylation biological_process GO:0034772 histone H4-K20 dimethylation GO:0034772 The modification of histone H4 by addition of two methyl groups to lysine at position 20 of the histone. GOC:mah The modification of a histone by addition of one or more methyl groups to a lysine residue. biological_process GO:0034968 histone lysine methylation GO:0034968 The modification of a histone by addition of one or more methyl groups to a lysine residue. GOC:mah GOC:pr The modification of a histone by addition of a methyl group to an arginine residue. biological_process GO:0034969 histone arginine methylation GO:0034969 The modification of a histone by addition of a methyl group to an arginine residue. GOC:mah Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD. https://github.com/geneontology/go-ontology/issues/22295 Reactome:R-HSA-3371467 Reactome:R-HSA-5211239 Reactome:R-HSA-5685953 Reactome:R-HSA-5688289 Reactome:R-HSA-5688294 Reactome:R-HSA-9620532 Reactome:R-HSA-9667952 molecular_function GO:0034979 NAD-dependent protein deacetylase activity GO:0034979 Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD. GOC:BHF GOC:mah PMID:28450737 Reactome:R-HSA-3371467 SIRT1 deacetylates HSF1 Reactome:R-HSA-5211239 SIRT1 deacetylates TAF1B in SL1 complex Reactome:R-HSA-5685953 SIRT6 deacetylates RBBP8 Reactome:R-HSA-5688289 SIRT3 deacetylates ACCS2, GLUD, IDH2, SOD2 Reactome:R-HSA-5688294 SIRT5 deacetylates Cytochrome C Reactome:R-HSA-9620532 SIRT1,SIRT3 deacetylate FOXO3 Reactome:R-HSA-9667952 ANKLE2 is deacetylated by SIRT2 true true Binds to and modulates the activity of histone deacetylase. molecular_function GO:0035033 See also the molecular function term 'histone deacetylase activity ; GO:0004407'. histone deacetylase regulator activity GO:0035033 Binds to and modulates the activity of histone deacetylase. GOC:bf Binds to and modulates the activity of histone acetyltransferase. histone acetylase regulator activity molecular_function GO:0035034 See also the molecular function term 'histone acetyltransferase activity ; GO:0004402'. histone acetyltransferase regulator activity GO:0035034 Binds to and modulates the activity of histone acetyltransferase. GOC:bf Binding to an histone acetyltransferase. histone acetylase binding molecular_function GO:0035035 histone acetyltransferase binding GO:0035035 Binding to an histone acetyltransferase. GOC:bf A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the Drosophila brm (brahma) or mammalian SMARCA2/BAF190B/BRM gene, or an ortholog thereof. BRM complex cellular_component GO:0035060 brahma complex GO:0035060 A SWI/SNF-type complex that contains 8 to 14 proteins, including both conserved (core) and nonconserved components; contains the ATPase product of the Drosophila brm (brahma) or mammalian SMARCA2/BAF190B/BRM gene, or an ortholog thereof. GOC:bhm PMID:10809665 PMID:12482982 Binding to a histone in which a residue has been modified by methylation. molecular_function GO:0035064 methylated histone binding GO:0035064 Binding to a histone in which a residue has been modified by methylation. GOC:bf PMID:14585615 Any process that modulates the frequency, rate or extent of the addition of an acetyl group to a histone protein. biological_process GO:0035065 regulation of histone acetylation GO:0035065 Any process that modulates the frequency, rate or extent of the addition of an acetyl group to a histone protein. GOC:bf Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein. up regulation of histone acetylation up-regulation of histone acetylation upregulation of histone acetylation activation of histone acetylation stimulation of histone acetylation biological_process GO:0035066 positive regulation of histone acetylation GO:0035066 Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein. GOC:bf true A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins. cellular_component GO:0035097 histone methyltransferase complex GO:0035097 A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins. GOC:bf A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4. Extra Sex Combs/Enhancer of Zeste complex PRC2 complex cellular_component GO:0035098 ESC/E(Z) complex GO:0035098 A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4. GOC:bf GOC:sp PMID:12408863 PMID:12408864 PMID:20064375 PRC2 complex GOC:sp PMID:20064375 A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling. Polycomb repressive complex 1 cellular_component GO:0035102 In Drosophila the core subunits are Pc (Polycomb), Psc (Posterior sex combs), Ph (Polyhomeotic) and Sce (Sex comb extra). In mammals, which have several orthologs for each of the Drosophila core proteins, a family of distinct PRC1-like complexes seem to exist which contain at least some PcG proteins in mutually exclusive manner. PRC1 complex GO:0035102 A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling. GOC:bf PMID:10412979 Catalysis of the transfer of a phosphate group to a histone. molecular_function GO:0035173 histone kinase activity GO:0035173 Catalysis of the transfer of a phosphate group to a histone. GOC:bf A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60). TIP60 histone acetylase complex TIP60 histone acetyltransferase complex cellular_component GO:0035267 NuA4 histone acetyltransferase complex GO:0035267 A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60). GOC:ecd PMID:10966108 PMID:14966270 The removal of the ubiquitin group from a monoubiquitinated protein. bf 2010-05-04T04:28:38Z monoubiquitinated protein deubiquitinylation monoubiquitinated protein deubiquitylation biological_process GO:0035520 monoubiquitinated protein deubiquitination GO:0035520 The removal of the ubiquitin group from a monoubiquitinated protein. GOC:bf The removal of the ubiquitin group from a monoubiquitinated histone protein. bf 2010-05-04T04:32:04Z monoubiquitinated histone deubiquitinylation monoubiquitinated histone deubiquitylation biological_process GO:0035521 monoubiquitinated histone deubiquitination GO:0035521 The removal of the ubiquitin group from a monoubiquitinated histone protein. GOC:bf PMID:20436459 The removal of the ubiquitin group from a monoubiquitinated histone H2A protein. bf 2010-05-04T04:32:53Z monoubiquitinated histone H2A deubiquitinylation monoubiquitinated histone H2A deubiquitylation biological_process GO:0035522 monoubiquitinated histone H2A deubiquitination GO:0035522 The removal of the ubiquitin group from a monoubiquitinated histone H2A protein. GOC:bf PMID:18226187 PMID:20436459 Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. bf 2010-05-19T10:28:36Z biological_process GO:0035561 regulation of chromatin binding GO:0035561 Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. GOC:bf PMID:20404130 Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. bf 2010-05-19T10:29:41Z biological_process GO:0035563 positive regulation of chromatin binding GO:0035563 Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. GOC:bf PMID:20404130 Catalysis of the removal of the methyl group from a modified lysine residue at position 20 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 bf 2010-08-13T10:51:13Z Reactome:R-HSA-2172678 histone H4-K20 demethylase activity histone H4-methyl-lysine-20 demethylase activity histone H4K20me demethylase activity histone demethylase activity (H4-K20 specific) histone demethylase activity (H4K20-specific) molecular_function GO:0035575 histone H4K20 demethylase activity GO:0035575 Catalysis of the removal of the methyl group from a modified lysine residue at position 20 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:20622853 PMID:26214369 PMID:32209475 Reactome:R-HSA-2172678 PHF8 demethylates histone H4K20me1 The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a protein amino acid. bf 2010-11-15T11:06:15Z protein amino acid deacylation biological_process GO:0035601 protein deacylation GO:0035601 The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a protein amino acid. GOC:se PMID:12080046 protein amino acid deacylation GOC:se Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 17) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 17). This reaction is the addition of a methyl group to the arginine residue at position 17 of histone H3. bf 2011-01-19T10:41:43Z histone methylase activity (H3-R17 specific) histone methyltransferase activity (H3-R17 specific) histone-H3R17 methyltransferase activity histone-arginine N-methyltransferase activity (H3-R17 specific) molecular_function GO:0035642 histone H3R17 methyltransferase activity GO:0035642 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 17) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 17). This reaction is the addition of a methyl group to the arginine residue at position 17 of histone H3. GOC:sp PMID:11341840 histone methylase activity (H3-R17 specific) GOC:bf histone-arginine N-methyltransferase activity (H3-R17 specific) GOC:bf Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule. bf 2012-01-17T04:20:34Z molecular_function GO:0036094 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule binding GO:0036094 Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:pm The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). https://github.com/geneontology/go-ontology/issues/23112 bf 2012-04-26T01:47:12Z GO:0006464 cellular protein modification process process resulting in protein modification protein modification biological_process GO:0036211 protein modification process GO:0036211 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). GOC:bf GOC:jl protein modification GOC:bf Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 14) = CoA + histone H3 N6-acetyl-L-lysine (position 14). bf 2013-08-21T10:03:10Z histone H3-K14 acetyltransferase activity histone acetylase activity (H3-K14 specific) histone acetyltransferase activity (H3-K14 specific) histone lysine N-acetyltransferase activity (H3-K14 specific) molecular_function GO:0036408 histone H3K14 acetyltransferase activity GO:0036408 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 14) = CoA + histone H3 N6-acetyl-L-lysine (position 14). GOC:vw PMID:21289066 histone lysine N-acetyltransferase activity (H3-K14 specific) GOC:bf A protein complex that can catalyze the acetylation of lysine at position 14 in histone H3. bf 2013-08-21T10:06:34Z H3-K14 histone acetyltransferase complex histone H3 Lys 14 (H3K14) acetyltransferase complex histone H3K14 acetyltransferase complex histone acetyltransferase complex (H3-K14 specific) cellular_component GO:0036409 histone H3-K14 acetyltransferase complex GO:0036409 A protein complex that can catalyze the acetylation of lysine at position 14 in histone H3. GOC:vw PMID:21289066 H3-K14 histone acetyltransferase complex GOC:bf histone H3 Lys 14 (H3K14) acetyltransferase complex PMID:21289066 histone H3K14 acetyltransferase complex PMID:21289066 histone acetyltransferase complex (H3-K14 specific) GOC:bf Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. regulation of meiosis biological_process GO:0040020 regulation of meiotic nuclear division GO:0040020 Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. GOC:ems GOC:ma regulation of meiosis GOC:vw A process that modulates the frequency, rate or extent of gene expression through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine methylation of DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal. https://github.com/geneontology/go-ontology/issues/22201 https://github.com/geneontology/go-ontology/issues/24794 regulation of gene expression, epigenetic biological_process GO:0040029 epigenetic regulation of gene expression GO:0040029 A process that modulates the frequency, rate or extent of gene expression through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine methylation of DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal. PMID:10521337 PMID:11498582 PMID:22243696 PMID:34414474 Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or a lysine residue. https://github.com/geneontology/go-ontology/issues/22588 https://github.com/geneontology/go-ontology/issues/24397 histone N-methyltransferase activity histone methylase activity molecular_function GO:0042054 histone methyltransferase activity GO:0042054 Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or a lysine residue. GOC:curators histone methylase activity GOC:mah Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus. regulation of protein import into cell nucleus regulation of protein transport from cytoplasm to nucleus regulation of protein-nucleus import biological_process GO:0042306 regulation of protein import into nucleus GO:0042306 Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus. GOC:jl Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus. positive regulation of protein import into cell nucleus positive regulation of protein transport from cytoplasm to nucleus positive regulation of protein-nucleus import up regulation of protein import into nucleus up-regulation of protein import into nucleus upregulation of protein import into nucleus activation of protein import into nucleus stimulation of protein import into nucleus biological_process GO:0042307 positive regulation of protein import into nucleus GO:0042307 Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. down regulation of protein import into nucleus down-regulation of protein import into nucleus downregulation of protein import into nucleus negative regulation of protein import into cell nucleus negative regulation of protein transport from cytoplasm to nucleus negative regulation of protein-nucleus import inhibition of protein import into nucleus biological_process GO:0042308 negative regulation of protein import into nucleus GO:0042308 Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus. GOC:jl Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaryotic or archaeal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in gene regulation and DNA replication. They may be chemically modified (methylated, acetlyated and others) to regulate gene transcription. https://github.com/geneontology/go-ontology/issues/23106 molecular_function histone-specific chaperone activity GO:0042393 histone binding GO:0042393 Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaryotic or archaeal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in gene regulation and DNA replication. They may be chemically modified (methylated, acetlyated and others) to regulate gene transcription. GOC:jl PMID:16209651 PMID:30212449 PMID:9305837 An intranuclear focus at which aggregated proteins have been sequestered. cellular_component GO:0042405 nuclear inclusion body GO:0042405 An intranuclear focus at which aggregated proteins have been sequestered. GOC:jl Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3. molecular_function GO:0042578 phosphoric ester hydrolase activity GO:0042578 Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3. GOC:jl Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group to the lysine residue at position 20 of the histone H4 protein. histone H4K20 methylase activity Reactome:R-HSA-2301205 Reactome:R-HSA-5682965 histone H4 lysine 20-specific methyltransferase activity histone H4K20 methylation histone lysine N-methyltransferase activity (H4-K20 specific) histone methylase activity (H4-K20 specific) histone methyltransferase activity (H4-K20 specific) histone-H4K20 methyltransferase activity molecular_function GO:0042799 Note that in some species, the methyl group may be added to a lysine in a slightly different position of the histone H4 protein, but that this term still applies. histone H4K20 methyltransferase activity GO:0042799 Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group to the lysine residue at position 20 of the histone H4 protein. PMID:12086618 Reactome:R-HSA-2301205 SETD8 monomethylates histone H4 Reactome:R-HSA-5682965 WHSC1 dimethylates histone H4 on lysine K21 at DSBs Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of up to three methyl groups to the lysine residue at position 4 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/24866 Reactome:R-HSA-1214188 Reactome:R-HSA-3364026 Reactome:R-HSA-8865498 Reactome:R-HSA-8936481 Reactome:R-HSA-8936621 Reactome:R-HSA-8937016 Reactome:R-HSA-8937050 histone H3 lysine 4-specific methyltransferase activity histone H3K4 methylase activity histone lysine N-methyltransferase activity (H3-K4 specific) histone methylase activity (H3-K4 specific) histone methyltransferase activity (H3-K4 specific) histone-H3K4 methyltransferase activity molecular_function GO:0042800 Note that in some species, the methyl group may be added to a lysine in a slightly different position of the histone H3 protein, but that this term still applies. histone H3K4 methyltransferase activity GO:0042800 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of up to three methyl groups to the lysine residue at position 4 of the histone H3 protein. PMID:12086618 Reactome:R-HSA-1214188 PRDM9 trimethylates histone H3 Reactome:R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene Reactome:R-HSA-8865498 KMT2A trimethylates nucleosomes at the SPI1 gene locus producing H3K4Me3 mark Reactome:R-HSA-8936481 Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter Reactome:R-HSA-8936621 Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter Reactome:R-HSA-8937016 Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter Reactome:R-HSA-8937050 Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter histone methylase activity (H3-K4 specific) GOC:mah Binding to histone deacetylase. molecular_function GO:0042826 histone deacetylase binding GO:0042826 Binding to histone deacetylase. GOC:jl Binding to a nuclear retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily. https://github.com/geneontology/go-ontology/issues/16717 retinoic acid receptor binding RAR binding molecular_function GO:0042974 nuclear retinoic acid receptor binding GO:0042974 Binding to a nuclear retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily. GOC:jl PMID:12476796 A epigenetic process that happens during embryonic development that modulates gene expression potential at later stages of development of the organism, including the adult. Epigenetic regulation takes place via chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine DNA methylation. biological_process DNA methylation involved in embryo development de novo DNA methylation epigenetic regulation of embryonic gene expression GO:0043045 post-fertilization epigenetic regulation of gene expression GO:0043045 A epigenetic process that happens during embryonic development that modulates gene expression potential at later stages of development of the organism, including the adult. Epigenetic regulation takes place via chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine DNA methylation. GOC:go_curators PMID:12138111 PMID:22868271 The nucleus of a germ cell, a reproductive cell in multicellular organisms. germ-cell nucleus cellular_component GO:0043073 germ cell nucleus GO:0043073 The nucleus of a germ cell, a reproductive cell in multicellular organisms. CL:0000586 GOC:go_curators Any process that activates or increases the activity of an enzyme. GO:0048554 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity GO:0043085 Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0034960 GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process GO:0043170 The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 A multisubunit complex that catalyzes the acetylation of histones H4 and H2A. H4/H2A HAT complex cellular_component GO:0043189 H4/H2A histone acetyltransferase complex GO:0043189 A multisubunit complex that catalyzes the acetylation of histones H4 and H2A. GOC:mah GOC:rb Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle GO:0043226 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle GO:0043227 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle biological condensate cellular_component GO:0043228 non-membrane-bounded organelle GO:0043228 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle GO:0043229 Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle GO:0043231 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle GO:0043232 Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators true The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. biological_process GO:0043412 macromolecule modification GO:0043412 The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties. GOC:go_curators The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. biological_process GO:0043414 macromolecule methylation GO:0043414 The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. GOC:go_curators An endoplasmic reticulum protein-containing complex that is conserved in eukaryotics and that mediates the insertion of tail-anchored proteins into the ER membrane. In yeast, includes Get1p, Get2p and Get3p proteins. https://github.com/geneontology/go-ontology/issues/20244 cellular_component GO:0043529 GET complex GO:0043529 An endoplasmic reticulum protein-containing complex that is conserved in eukaryotics and that mediates the insertion of tail-anchored proteins into the ER membrane. In yeast, includes Get1p, Get2p and Get3p proteins. GOC:krc GOC:vw PMID:16269340 PMID:18724936 PMID:32910895 The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid. protein amino acid acylation biological_process GO:0043543 protein acylation GO:0043543 The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid. GOC:jl protein amino acid acylation GOC:bf Heterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK. Ku70:Ku80 heterodimer cellular_component GO:0043564 Ku70:Ku80 complex GO:0043564 Heterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK. PMID:12518983 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence specific DNA binding molecular_function GO:0043565 sequence-specific DNA binding GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GOC:jl The Y-shaped region of a nuclear replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. cellular_component GO:0043596 nuclear replication fork GO:0043596 The Y-shaped region of a nuclear replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. GOC:jl GOC:mtg_sensu The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome. Wikipedia:Posttranslational_modification PTM post-translational amino acid modification post-translational modification posttranslational amino acid modification posttranslational modification posttranslational protein modification biological_process GO:0043687 This term should only be used to annotate a protein modification process that occurs after the protein has been released from the ribosome, and is therefore strictly post-translational. Modification of a free protein (one not attached to a ribosome) and modification of a C-terminal residue are post-translational processes. Some protein modifications occur while the protein is still in the ribosome but before translation has been completed; these modification processes are considered co-translational and should not be annotated using this term. post-translational protein modification GO:0043687 The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome. GOC:jsg Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 mah 2010-09-08T10:01:42Z GO:0034600 GO:0034621 GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization protein-containing complex subunit organization GO:0043933 protein-containing complex organization GO:0043933 Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. GOC:mah protein complex subunit organisation GOC:mah The modification of histone H3 by the addition of an acetyl group. biological_process GO:0043966 histone H3 acetylation GO:0043966 The modification of histone H3 by the addition of an acetyl group. GOC:jl The modification of histone H4 by the addition of an acetyl group. biological_process GO:0043967 histone H4 acetylation GO:0043967 The modification of histone H4 by the addition of an acetyl group. GOC:jl The modification of histone H2A by the addition of an acetyl group. biological_process GO:0043968 histone H2A acetylation GO:0043968 The modification of histone H2A by the addition of an acetyl group. GOC:jl The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone. histone H4 acetylation at K5 biological_process GO:0043981 histone H4-K5 acetylation GO:0043981 The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone. GOC:jl The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone. histone H4 acetylation at K8 biological_process GO:0043982 histone H4-K8 acetylation GO:0043982 The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone. GOC:jl The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone. histone H4 acetylation at K12 biological_process GO:0043983 histone H4-K12 acetylation GO:0043983 The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone. GOC:jl The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone. histone H4 acetylation at K16 biological_process GO:0043984 histone H4-K16 acetylation GO:0043984 The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone. GOC:jl The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone. histone H4 R3 methylation histone H4 methylation at R3 histone H4R3me biological_process GO:0043985 histone H4-R3 methylation GO:0043985 The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone. GOC:mah Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 9) = CoA + histone H3 N6-acetyl-L-lysine (position 9). histone H3-K9 acetyltransferase activity histone acetylase activity (H3-K9 specific) histone acetyltransferase activity (H3-K9 specific) histone lysine N-acetyltransferase activity (H3-K9 specific) molecular_function GO:0043992 histone H3K9 acetyltransferase activity GO:0043992 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 9) = CoA + histone H3 N6-acetyl-L-lysine (position 9). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 18) = CoA + histone H3 N6-acetyl-L-lysine (position 18). histone H3-K18 acetyltransferase activity histone acetylase activity (H3-K18 specific) histone acetyltransferase activity (H3-K18 specific) histone lysine N-acetyltransferase activity (H3-K18 specific) molecular_function GO:0043993 histone H3K18 acetyltransferase activity GO:0043993 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 18) = CoA + histone H3 N6-acetyl-L-lysine (position 18). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 23) = CoA + histone H3 N6-acetyl-L-lysine (position 23). histone H3-K23 acetyltransferase activity histone acetylase activity (H3-K23 specific) histone acetyltransferase activity (H3-K23 specific) histone lysine N-acetyltransferase activity (H3-K23 specific) molecular_function GO:0043994 histone H3K23 acetyltransferase activity GO:0043994 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 23) = CoA + histone H3 N6-acetyl-L-lysine (position 23). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 5) = CoA + histone H4 N6-acetyl-L-lysine (position 5). histone acetylase activity (H4-K5 specific) histone acetyltransferase activity (H4-K5 specific) histone lysine N-acetyltransferase activity (H4-K5 specific) molecular_function GO:0043995 histone H4K5 acetyltransferase activity GO:0043995 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 5) = CoA + histone H4 N6-acetyl-L-lysine (position 5). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 8) = CoA + histone H4 N6-acetyl-L-lysine (position 8). histone acetylase activity (H4-K8 specific) histone acetyltransferase activity (H4-K8 specific) histone lysine N-acetyltransferase activity (H4-K8 specific) molecular_function GO:0043996 histone H4K8 acetyltransferase activity GO:0043996 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 8) = CoA + histone H4 N6-acetyl-L-lysine (position 8). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 12) = CoA + histone H4 N6-acetyl-L-lysine (position 12). histone H4-K12 acetyltransferase activity histone acetylase activity (H4-K12 specific) histone acetyltransferase activity (H4-K12 specific) histone lysine N-acetyltransferase activity (H4-K12 specific) molecular_function GO:0043997 histone H4K12 acetyltransferase activity GO:0043997 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 12) = CoA + histone H4 N6-acetyl-L-lysine (position 12). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine = CoA + histone H2A N6-acetyl-L-lysine. H2A histone acetylase activity H2A histone acetyltransferase activity H2A histone lysine N-acetyltransferase activity molecular_function GO:0043998 histone H2A acetyltransferase activity GO:0043998 Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine = CoA + histone H2A N6-acetyl-L-lysine. EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine (position 5) = CoA + histone H2A N6-acetyl-L-lysine (position 5). https://github.com/geneontology/go-ontology/issues/23793 histone H2A-K5 acetyltransferase activity histone acetylase activity (H2A-K5 specific) histone acetyltransferase activity (H2A-K5 specific) histone lysine N-acetyltransferase activity (H2A-K5 specific) molecular_function GO:0043999 Note that in yeast, this is corresponds to H2AK4. histone H2AK5 acetyltransferase activity GO:0043999 Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine (position 5) = CoA + histone H2A N6-acetyl-L-lysine (position 5). EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine = CoA + histone H2B N6-acetyl-L-lysine. H2B histone acetylase activity H2B histone acetyltransferase activity H2B histone lysine N-acetyltransferase activity molecular_function GO:0044013 histone H2B acetyltransferase activity GO:0044013 Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine = CoA + histone H2B N6-acetyl-L-lysine. EC:2.3.1.48 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 4) = CoA + histone H3 N6-acetyl-L-lysine (position 4). histone H3-K4 acetyltransferase activity histone acetylase activity (H3-K4 specific) histone acetyltransferase activity (H3-K4 specific) histone lysine N-acetyltransferase activity (H3-K4 specific) molecular_function GO:0044016 histone H3K4 acetyltransferase activity GO:0044016 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 4) = CoA + histone H3 N6-acetyl-L-lysine (position 4). EC:2.3.1.48 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H4, producing histone H4R3me. histone H4KR3 methylation histone H4R3 arginine methylase activity histone methylase activity (H4-R3 specific) histone methyltransferase activity (H4-R3 specific) histone-arginine N-methyltransferase activity (H4-R3 specific) molecular_function GO:0044020 histone H4R3 methyltransferase activity GO:0044020 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H4, producing histone H4R3me. GOC:mah PMID:17898714 histone methylase activity (H4-R3 specific) GOC:mah An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes. https://github.com/geneontology/go-ontology/issues/24543 https://github.com/geneontology/go-ontology/issues/24711 maintenance of DNA methylation DNA hypermethylation of CpG island epigenetic regulation of gene expression via CpG island hypermethylation hypermethylation of CpG island negative regulation of gene expression via CpG island hypermethylation negative regulation of gene expression via chromosomal DNA cytosine methylation biological_process GO:0044027 negative regulation of gene expression via CpG island methylation GO:0044027 An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes. GOC:jl PMID:11898023 Wikipedia:Cpg_island An epigenetic gene regulation mechanism that positively regulates gene expression by demethylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes. https://github.com/geneontology/go-ontology/issues/24543 DNA hypomethylation of CpG island hypomethylation of CpG island biological_process GO:0044029 positive regulation of gene expression via CpG island demethylation GO:0044029 An epigenetic gene regulation mechanism that positively regulates gene expression by demethylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes. GOC:jl PMID:36150101 Wikipedia:Cpg_island Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. biological_process GO:0044030 regulation of DNA methylation GO:0044030 Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GOC:jl Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044087 regulation of cellular component biogenesis GO:0044087 Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044089 positive regulation of cellular component biogenesis GO:0044089 Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jl 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function GO:0044093 Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 14 of the histone. jl 2009-08-11T03:40:43Z histone H3 acetylation at K14 histone H3K14 acetylation biological_process GO:0044154 histone H3-K14 acetylation GO:0044154 The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 14 of the histone. GOC:jl GOC:lb PMID:17194708 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular metabolic process GO:0044237 The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism biological_process GO:0044238 primary metabolic process GO:0044238 The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residues at several positions. In human, it contains the catalytic subunit MOF, NSL1/KIAA1267, NSL2/KANSL2, NSL3/KANSL3, MCRS1, PHF20, OGT1, WDR5 and HCF1. jl 2012-03-22T12:49:18Z non-specific lethal complex cellular_component GO:0044545 NSL complex GO:0044545 A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residues at several positions. In human, it contains the catalytic subunit MOF, NSL1/KIAA1267, NSL2/KANSL2, NSL3/KANSL3, MCRS1, PHF20, OGT1, WDR5 and HCF1. GOC:lb PMID:20018852 A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL1 or MLL2 in human, or equivalent in other species. jl 2012-08-07T14:44:12Z Trx-containing complex cellular_component GO:0044665 MLL1/2 complex GO:0044665 A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL1 or MLL2 in human, or equivalent in other species. GOC:sart PMID:21875999 A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL3 or MLL4 in mammals, or equivalent in other species. jl 2012-08-07T14:46:40Z Trr/COMPASS-like complex cellular_component GO:0044666 MLL3/4 complex GO:0044666 A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL3 or MLL4 in mammals, or equivalent in other species. GOC:sart PMID:21875999 true Binding to a macromolecular complex. jl 2014-12-16T11:38:58Z GO:0032403 protein complex binding molecular_function macromolecular complex binding GO:0044877 protein-containing complex binding GO:0044877 Binding to a macromolecular complex. GOC:jl The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents. Wikipedia:Pronucleus cellular_component GO:0045120 pronucleus GO:0045120 The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents. ISBN:0198506732 The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization GO:0045184 The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away. active protein retrieval protein retention protein sequestering biological_process maintenance of protein localization GO:0045185 maintenance of protein location GO:0045185 Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away. GOC:bf maintenance of protein localization GOC:dph GOC:tb A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. cellular_component GO:0045253 See also the cellular component term 'cytosolic pyruvate dehydrogenase complex ; GO:0045250'. pyruvate dehydrogenase (lipoamide) phosphatase complex GO:0045253 A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PMID:9395502 Binding to uan nmethylated CpG motif. Unmethylated CpG dinucleotides are often associated with gene promoters. molecular_function GO:0045322 unmethylated CpG binding GO:0045322 Binding to uan nmethylated CpG motif. Unmethylated CpG dinucleotides are often associated with gene promoters. GOC:ai PMID:10688657 Any process that activates or increases the frequency, rate or extent of DNA replication. up regulation of DNA replication up-regulation of DNA replication upregulation of DNA replication activation of DNA replication stimulation of DNA replication biological_process GO:0045740 positive regulation of DNA replication GO:0045740 Any process that activates or increases the frequency, rate or extent of DNA replication. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. down regulation of progression through cell cycle down-regulation of progression through cell cycle downregulation of progression through cell cycle negative regulation of cell cycle progression negative regulation of progression through cell cycle inhibition of progression through cell cycle biological_process GO:0045786 negative regulation of cell cycle GO:0045786 Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the rate or extent of progression through the cell cycle. positive regulation of cell cycle progression positive regulation of progression through cell cycle up regulation of progression through cell cycle up-regulation of progression through cell cycle upregulation of progression through cell cycle activation of progression through cell cycle stimulation of progression through cell cycle biological_process GO:0045787 positive regulation of cell cycle GO:0045787 Any process that activates or increases the rate or extent of progression through the cell cycle. GOC:go_curators positive regulation of progression through cell cycle GOC:dph GOC:tb An epigenetic process that silences gene expression at specific genomic regions through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the cytosine DNA methylation. https://github.com/geneontology/go-ontology/issues/22201 down regulation of gene expression, epigenetic down-regulation of gene expression, epigenetic downregulation of gene expression, epigenetic inhibition of gene expression, epigenetic biological_process gene silencing GO:0045814 negative regulation of gene expression, epigenetic GO:0045814 An epigenetic process that silences gene expression at specific genomic regions through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the cytosine DNA methylation. PMID:22243696 An epigenetic mechanism of regulation of gene expression that involves chromatin remodeling to capacitate gene expression by either modifying the chromatin fiber, the nucleosomal histones, or the DNA. https://github.com/geneontology/go-ontology/issues/21730 https://github.com/geneontology/go-ontology/issues/22012 https://github.com/geneontology/go-ontology/issues/23696 GO:0048096 chromatin-mediated maintenance of transcription epigenetic maintenance of chromatin in transcription-competent conformation maintenance of chromatin in transcription-competent conformation positive regulation of gene expression, epigenetic transciptional initiation-coupled chromatin remodeling transcription initiation coupled chromatin remodeling transcriptional initiation-coupled chromatin remodeling up regulation of gene expression, epigenetic up-regulation of gene expression, epigenetic upregulation of gene expression, epigenetic biological_process DNA replication-independent chromatin organization activation of gene expression, epigenetic euchromatin assembly euchromatin organisation euchromatin organization long-term maintenance of gene activation stimulation of gene expression, epigenetic GO:0045815 This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. Do not confuse with GO:0140673 ; transcriptional elongation-coupled chromatin remodeling, which describes the reforming of chromatin after RNA polymerase II passage. transcription initiation-coupled chromatin remodeling GO:0045815 An epigenetic mechanism of regulation of gene expression that involves chromatin remodeling to capacitate gene expression by either modifying the chromatin fiber, the nucleosomal histones, or the DNA. PMID:34414474 Any process that activates or increases the frequency, rate or extent of meiosis. positive regulation of meiosis up regulation of meiosis up-regulation of meiosis upregulation of meiosis activation of meiosis stimulation of meiosis biological_process GO:0045836 positive regulation of meiotic nuclear division GO:0045836 Any process that activates or increases the frequency, rate or extent of meiosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of mitosis. positive regulation of mitosis up regulation of mitosis up-regulation of mitosis upregulation of mitosis activation of mitosis mitogenic activity stimulation of mitosis biological_process GO:0045840 positive regulation of mitotic nuclear division GO:0045840 Any process that activates or increases the frequency, rate or extent of mitosis. GOC:go_curators Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process GO:0045934 Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process GO:0045935 Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process GO:0046483 The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198506732 A ribonucleoprotein complex that is formed by the association of the U4/U6 and U5 snRNPs. U4/U6.U5 snRNP complex cellular_component GO:0046540 U4/U6 x U5 tri-snRNP complex GO:0046540 A ribonucleoprotein complex that is formed by the association of the U4/U6 and U5 snRNPs. GOC:krc GOC:pr ISBN:0879695897 PMID:11867543 Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. biological_process GO:0046822 regulation of nucleocytoplasmic transport GO:0046822 Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. down regulation of nucleocytoplasmic transport down-regulation of nucleocytoplasmic transport downregulation of nucleocytoplasmic transport inhibition of nucleocytoplasmic transport biological_process GO:0046823 negative regulation of nucleocytoplasmic transport GO:0046823 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus. GOC:bf Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. up regulation of nucleocytoplasmic transport up-regulation of nucleocytoplasmic transport upregulation of nucleocytoplasmic transport activation of nucleocytoplasmic transport stimulation of nucleocytoplasmic transport biological_process GO:0046824 positive regulation of nucleocytoplasmic transport GO:0046824 Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm. GOC:bf Any process that modulates the frequency, rate or extent of the directed movement of proteins from the nucleus to the cytoplasm. regulation of protein export from cell nucleus regulation of protein export out of nucleus regulation of protein transport from nucleus to cytoplasm regulation of protein-nucleus export biological_process GO:0046825 regulation of protein export from nucleus GO:0046825 Any process that modulates the frequency, rate or extent of the directed movement of proteins from the nucleus to the cytoplasm. GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm. down regulation of protein export from nucleus down-regulation of protein export from nucleus downregulation of protein export from nucleus negative regulation of protein export from cell nucleus negative regulation of protein export out of nucleus negative regulation of protein transport from nucleus to cytoplasm negative regulation of protein-nucleus export inhibition of protein export from nucleus biological_process GO:0046826 negative regulation of protein export from nucleus GO:0046826 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm. GOC:bf Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm. positive regulation of protein export from cell nucleus positive regulation of protein export out of nucleus positive regulation of protein transport from nucleus to cytoplasm positive regulation of protein-nucleus export up regulation of protein export from nucleus up-regulation of protein export from nucleus upregulation of protein export from nucleus activation of protein export from nucleus stimulation of protein export from nucleus biological_process GO:0046827 positive regulation of protein export from nucleus GO:0046827 Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm. GOC:bf Any process that modulates the frequency, rate or extent of the directed movement of RNA from the nucleus to the cytoplasm. regulation of RNA export from cell nucleus regulation of RNA export out of nucleus regulation of RNA transport from nucleus to cytoplasm regulation of RNA-nucleus export biological_process GO:0046831 regulation of RNA export from nucleus GO:0046831 Any process that modulates the frequency, rate or extent of the directed movement of RNA from the nucleus to the cytoplasm. GOC:bf The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport GO:0046907 intracellular transport GO:0046907 The directed movement of substances within a cell. GOC:ai single organism intracellular transport GOC:TermGenie Binding to a nuclear retinoid X receptor. https://github.com/geneontology/go-ontology/issues/16717 retinoid X receptor binding RXR binding molecular_function GO:0046965 nuclear retinoid X receptor binding GO:0046965 Binding to a nuclear retinoid X receptor. GOC:ai Binding to a nuclear thyroid hormone receptor. https://github.com/geneontology/go-ontology/issues/16717 thyroid hormone receptor binding ligand-dependent thyroid hormone receptor interactor activity molecular_function GO:0046966 nuclear thyroid hormone receptor binding GO:0046966 Binding to a nuclear thyroid hormone receptor. GOC:ai Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein. Reactome:R-HSA-9604829 NAD-dependent H3-K9 histone deacetylase activity NAD-dependent histone deacetylase activity (H3-K9 specific) molecular_function GO:0046969 NAD-dependent histone H3K9 deacetylase activity GO:0046969 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein. PMID:28450737 Reactome:R-HSA-9604829 SIRT6 deacetylates histones at NOTCH1 and NOTCH4 gene promoters Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein. https://github.com/geneontology/go-ontology/issues/22676 NAD-dependent histone H4-K16 deacetylase activity NAD-dependent histone deacetylase activity (H4-K16 specific) molecular_function GO:0046970 NAD-dependent histone H4K16 deacetylase activity GO:0046970 Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein. GOC:vw PMID:28450737 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 16) = CoA + histone H4 N6-acetyl-L-lysine (position 16). This reaction represents the addition of an acetyl group to the lysine at position 16 of histone H4. histone acetylase activity (H4-K16 specific) histone acetyltransferase activity (H4-K16 specific) histone lysine acetyltransferase activity (H4-K16 specific) molecular_function GO:0046972 histone H4K16 acetyltransferase activity GO:0046972 Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 16) = CoA + histone H4 N6-acetyl-L-lysine (position 16). This reaction represents the addition of an acetyl group to the lysine at position 16 of histone H4. EC:2.3.1.48 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of up to three methyl groups to the lysine residue at position 9 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/22588 https://github.com/geneontology/go-ontology/issues/24337 Reactome:R-HSA-427336 Reactome:R-HSA-427527 histone H3K9 methylase activity histone lysine N-methyltransferase activity (H3-K9 specific) histone methylase activity (H3-K9 specific) histone methyltransferase activity (H3-K9 specific) histone-H3K9 methyltransferase activity molecular_function GO:0046974 histone H3K9 methyltransferase activity GO:0046974 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of up to three methyl groups to the lysine residue at position 9 of the histone H3 protein. GOC:ai Reactome:R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9. Reactome:R-HSA-427527 eNoSC dimethylates histone H3 at lysine-9 histone methylase activity (H3-K9 specific) GOC:mah Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group to the lysine residue at position 36 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/24337 histone H3K36 methylase activity histone lysine N-methyltransferase activity (H3-K36 specific) histone methylase activity (H3-K36 specific) histone methyltransferase activity (H3-K36 specific) histone-H3K36 methyltransferase activity molecular_function GO:0046975 histone H3K36 methyltransferase activity GO:0046975 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group to the lysine residue at position 36 of the histone H3 protein. GOC:ai histone methylase activity (H3-K36 specific) GOC:mah Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group to the lysine residue at position 27 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/24337 EC:2.1.1.356 Reactome:R-HSA-3240295 histone H3K27 methylase activity histone lysine N-methyltransferase activity (H3-K27 specific) histone methylase activity (H3-K27 specific) histone methylase activity (H3-K56 specific) histone methyltransferase activity (H3-K27 specific) histone-H3K27 methyltransferase activity molecular_function GO:0046976 histone H3K27 methyltransferase activity GO:0046976 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group to the lysine residue at position 27 of the histone H3 protein. GOC:ai Reactome:R-HSA-3240295 PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter histone methylase activity (H3-K27 specific) GOC:mah A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. COMPASS complex Set1/COMPASS complex Set1C cellular_component GO:0048188 Set1C/COMPASS complex GO:0048188 A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. PMID:11687631 PMID:11742990 PMID:11805083 PMID:12488447 PMID:18508253 PMID:18838538 COMPASS complex GOC:vw Set1/COMPASS complex GOC:mah Set1C GOC:vw The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission GO:0048285 The creation of two or more organelles by division of one organelle. GOC:jid Cytoplasm situated near, or occurring around, the nucleus. cellular_component GO:0048471 Note that this term should not be confused with the cellular component term 'nuclear membrane lumen ; GO:0005641', which has the synonym 'perinuclear space'. perinuclear region of cytoplasm GO:0048471 Cytoplasm situated near, or occurring around, the nucleus. GOC:jid Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process GO:0048518 Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process GO:0048519 Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process GO:0048522 Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process GO:0048523 Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Binding to a nuclear androgen receptor. https://github.com/geneontology/go-ontology/issues/16717 androgen receptor binding AR binding molecular_function GO:0050681 nuclear androgen receptor binding GO:0050681 Binding to a nuclear androgen receptor. GOC:ai Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process GO:0050789 Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity GO:0050790 Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process GO:0050794 Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport GO:0051049 Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport GO:0051050 Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport GO:0051051 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process GO:0051052 regulation of DNA metabolic process GO:0051052 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. down regulation of DNA metabolic process down-regulation of DNA metabolic process downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process GO:0051053 negative regulation of DNA metabolic process GO:0051053 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process GO:0051054 positive regulation of DNA metabolic process GO:0051054 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. biological_process GO:0051098 regulation of binding GO:0051098 Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process GO:0051099 positive regulation of binding GO:0051099 Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization GO:0051128 Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis GO:0051129 negative regulation of cellular component organization GO:0051129 Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive regulation of cellular component organization GO:0051130 Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah The directed movement of substances into, out of, or within the nucleus. Wikipedia:Nuclear_transport nucleus transport biological_process GO:0051169 nuclear transport GO:0051169 The directed movement of substances into, out of, or within the nucleus. GOC:ai The directed movement of substances into the nucleus. jl 2013-12-19T15:26:34Z GO:1902593 nuclear import nuclear translocation biological_process GO:0051170 import into nucleus GO:0051170 The directed movement of substances into the nucleus. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process GO:0051171 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process GO:0051172 negative regulation of nitrogen compound metabolic process GO:0051172 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process GO:0051173 positive regulation of nitrogen compound metabolic process GO:0051173 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization GO:0051179 Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products. Reactome:R-HSA-112120 Reactome:R-HSA-112121 Reactome:R-HSA-112124 Reactome:R-HSA-112125 molecular_function GO:0051213 dioxygenase activity GO:0051213 Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products. DOI:10.1016/S0040-4020(03)00944-X GOC:bf Reactome:R-HSA-112120 Oxidative demethylation of 3-meC damaged DNA by ALKBH2 Reactome:R-HSA-112121 Oxidative dealkylation of 1-etA damaged DNA By ALKBH2 Reactome:R-HSA-112124 Oxidative demethylation of 3-meC damaged DNA By ALKBH3 Reactome:R-HSA-112125 Oxidative dealkylation of 1-EtA damaged DNA by ABH3 Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport GO:0051222 Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051223 regulation of protein transport GO:0051223 Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport GO:0051224 Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation biological_process GO:0051234 establishment of localization GO:0051234 Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere. maintenance of localization retention sequestering storage biological_process GO:0051235 maintenance of location GO:0051235 Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere. GOC:ai GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032268 regulation of protein metabolism biological_process regulation of cellular protein metabolic process regulation of cellular protein metabolism GO:0051246 regulation of protein metabolic process GO:0051246 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032270 positive regulation of cellular protein metabolic process positive regulation of cellular protein metabolism positive regulation of protein metabolism up regulation of cellular protein metabolic process up regulation of protein metabolic process up-regulation of cellular protein metabolic process up-regulation of protein metabolic process upregulation of cellular protein metabolic process upregulation of protein metabolic process activation of cellular protein metabolic process activation of protein metabolic process stimulation of cellular protein metabolic process stimulation of protein metabolic process biological_process GO:0051247 positive regulation of protein metabolic process GO:0051247 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032269 down regulation of cellular protein metabolic process down regulation of protein metabolic process down-regulation of cellular protein metabolic process down-regulation of protein metabolic process downregulation of cellular protein metabolic process downregulation of protein metabolic process negative regulation of cellular protein metabolic process negative regulation of cellular protein metabolism negative regulation of protein metabolism inhibition of cellular protein metabolic process inhibition of protein metabolic process biological_process GO:0051248 negative regulation of protein metabolic process GO:0051248 Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. GOC:ai A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 GO:0006323 GO:0007001 GO:0051277 DNA condensation chromosome organisation DNA packaging biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization GO:0051276 A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. hydrolase regulator biological_process GO:0051336 regulation of hydrolase activity GO:0051336 Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. GOC:ai Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. hydrolase activator up regulation of hydrolase activity up-regulation of hydrolase activity upregulation of hydrolase activity activation of hydrolase activity stimulation of hydrolase activity biological_process GO:0051345 positive regulation of hydrolase activity GO:0051345 Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that modulates the rate or extent of progression through the meiotic cell cycle. meiotic cell cycle modulation meiotic cell cycle regulation modulation of meiotic cell cycle progression regulation of meiotic cell cycle progression regulation of progression through meiotic cell cycle biological_process meiotic cell cycle regulator GO:0051445 regulation of meiotic cell cycle GO:0051445 Any process that modulates the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. positive regulation of meiotic cell cycle progression positive regulation of progression through meiotic cell cycle up regulation of progression through meiotic cell cycle up-regulation of progression through meiotic cell cycle upregulation of progression through meiotic cell cycle activation of progression through meiotic cell cycle stimulation of progression through meiotic cell cycle biological_process GO:0051446 positive regulation of meiotic cell cycle GO:0051446 Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb positive regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus. maintenance of nuclear protein localization maintenance of protein location in cell nucleus nuclear protein retention nuclear protein sequestering nuclear protein sequestration protein retention in nucleus protein sequestration in nucleus protein storage in nucleus protein-nuclear retention sequestration of protein in nucleus storage of protein in nucleus biological_process maintenance of protein localization in nucleus GO:0051457 maintenance of protein location in nucleus GO:0051457 Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus. GOC:ai maintenance of protein localization in nucleus GOC:dph GOC:tb The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone. histone H3 K9 methylation histone H3K9me histone lysine H3 K9 methylation biological_process GO:0051567 histone H3-K9 methylation GO:0051567 The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone. GOC:ai GOC:pr The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone. histone H3 K4 methylation histone H3K4me histone lysine H3 K4 methylation biological_process GO:0051568 histone H3-K4 methylation GO:0051568 The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone. GOC:ai GOC:pr Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. biological_process GO:0051569 regulation of histone H3-K4 methylation GO:0051569 Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. GOC:ai Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. biological_process GO:0051570 regulation of histone H3-K9 methylation GO:0051570 Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. GOC:ai Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. up regulation of histone H3-K4 methylation up-regulation of histone H3-K4 methylation upregulation of histone H3-K4 methylation activation of histone H3-K4 methylation stimulation of histone H3-K4 methylation biological_process GO:0051571 positive regulation of histone H3-K4 methylation GO:0051571 Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. down regulation of histone H3-K4 methylation down-regulation of histone H3-K4 methylation downregulation of histone H3-K4 methylation inhibition of histone H3-K4 methylation biological_process GO:0051572 negative regulation of histone H3-K4 methylation GO:0051572 Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. down regulation of histone H3-K9 methylation down-regulation of histone H3-K9 methylation downregulation of histone H3-K9 methylation inhibition of histone H3-K9 methylation biological_process GO:0051573 negative regulation of histone H3-K9 methylation GO:0051573 Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. GOC:ai Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. up regulation of histone H3-K9 methylation up-regulation of histone H3-K9 methylation upregulation of histone H3-K9 methylation activation of histone H3-K9 methylation stimulation of histone H3-K9 methylation biological_process GO:0051574 positive regulation of histone H3-K9 methylation GO:0051574 Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3. GOC:ai Any process in which an organelle is transported to, and/or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/19809 establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization GO:0051640 Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation GOC:mah A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 cellular localization GO:0051641 A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. GOC:tb GOC:vw cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. cell nucleus localization establishment and maintenance of nucleus localization localization of nucleus nucleus localisation biological_process GO:0051647 nucleus localization GO:0051647 Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. GOC:ai nucleus localisation GOC:mah Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell GO:0051649 Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. cellular retention cellular sequestering cellular storage intracellular retention intracellular sequestering intracellular storage maintenance of intracellular localization maintenance of localization within cell retention within cell sequestering within cell storage within cell biological_process maintenance of cellular localization maintenance of localization in cell GO:0051651 maintenance of location in cell GO:0051651 Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere. GOC:ai maintenance of cellular localization GOC:dph GOC:tb maintenance of localization in cell GOC:dph GOC:tb Any process in which an organelle is maintained in a specific location within a cell and prevented from moving elsewhere. biological_process maintenance of organelle localization GO:0051657 maintenance of organelle location GO:0051657 Any process in which an organelle is maintained in a specific location within a cell and prevented from moving elsewhere. GOC:ai GOC:dph GOC:tb maintenance of organelle localization GOC:dph GOC:tb Any process in which the nucleus is maintained in a specific location within a cell and prevented from moving elsewhere. maintenance of cell nucleus location biological_process maintenance of nucleus localization GO:0051658 maintenance of nucleus location GO:0051658 Any process in which the nucleus is maintained in a specific location within a cell and prevented from moving elsewhere. GOC:ai GOC:dph GOC:tb maintenance of nucleus localization GOC:dph GOC:tb Catalysis of the reaction: S-adenosyl-L-methionine + CpG (in DNA) = S-adenosyl-L-homocysteine + 5-MeCpG (in DNA). Reactome:R-HSA-5334151 HpaII methylase HpaII' methylase M.BsuRIa M.BsuRIb molecular_function GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates GO:0051718 Catalysis of the reaction: S-adenosyl-L-methionine + CpG (in DNA) = S-adenosyl-L-homocysteine + 5-MeCpG (in DNA). EC:2.1.1.37 PMID:15689527 Reactome:R-HSA-5334151 DNMT1 methylates cytosine in hemimethylated DNA HpaII methylase EC:2.1.1.37 HpaII' methylase EC:2.1.1.37 M.BsuRIa EC:2.1.1.37 M.BsuRIb EC:2.1.1.37 Any process that modulates the rate or extent of progression through the cell cycle. GO:0000074 GO:0007050 GO:0071156 GO:0071157 GO:0071158 GO:0071850 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle arrest of mitotic cell cycle progression cell cycle arrest mitotic cell cycle arrest negative regulation of cell cycle arrest positive regulation of cell cycle arrest regulation of cell cycle arrest biological_process cell cycle regulator tumor suppressor GO:0051726 regulation of cell cycle GO:0051726 Any process that modulates the rate or extent of progression through the cell cycle. GOC:ai GOC:dph GOC:tb arrest of mitotic cell cycle progression GOC:mah Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. biological_process GO:0051783 regulation of nuclear division GO:0051783 Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. up regulation of nuclear division up-regulation of nuclear division upregulation of nuclear division activation of nuclear division stimulation of nuclear division biological_process GO:0051785 positive regulation of nuclear division GO:0051785 Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Catalysis of the removal of a methyl group from a modified lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 [histone-H3]-lysine-36 demethylase activity histone H3-K36 demethylase activity histone H3-lysine-36 demethylase activity histone H3-methyl-lysine-36 demethylase activity histone demethylase activity (H3-K36 specific) histone-lysine (H3-K36) demethylase activity histone-lysine demethylase activity (H3-K36 specific) histone-lysine(H3-K36) demethylase activity molecular_function GO:0051864 histone H3K36 demethylase activity GO:0051864 Catalysis of the removal of a methyl group from a modified lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:16362057 Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. biological_process GO:0051983 regulation of chromosome segregation GO:0051983 Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. up regulation of chromosome segregation up-regulation of chromosome segregation upregulation of chromosome segregation activation of chromosome segregation stimulation of chromosome segregation biological_process GO:0051984 positive regulation of chromosome segregation GO:0051984 Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. GO:0032947 binding, bridging molecular_function protein complex scaffold activity protein-containing complex scaffold activity GO:0060090 molecular adaptor activity GO:0060090 The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. GOC:mtg_MIT_16mar07 GOC:vw Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0060255 regulation of macromolecule metabolic process GO:0060255 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization GO:0060341 Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. dph 2009-05-18T02:12:13Z biological_process GO:0060623 regulation of chromosome condensation GO:0060623 Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:dph GOC:tb Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on either the paternal or maternal X-chromosome in the XX sex. dph 2009-08-11T10:47:30Z biological_process GO:0060816 random inactivation of X chromosome GO:0060816 Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on either the paternal or maternal X-chromosome in the XX sex. GOC:dph GOC:sdb_2009 GOC:tb PMID:32189388 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. jl 2010-02-08T02:43:11Z GO:0016044 GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization GO:0061024 membrane organization GO:0061024 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:dph GOC:tb membrane organisation GOC:mah membrane organization and biogenesis GOC:mah Any process that modulates the rate, frequency, or extent of rDNA heterochromatin formation. https://github.com/geneontology/go-ontology/issues/19238 dph 2010-07-14T09:04:16Z regulation of chromatin silencing at rDNA regulation of ribosomal DNA heterochromatin assembly biological_process GO:0061187 regulation of rDNA heterochromatin formation GO:0061187 Any process that modulates the rate, frequency, or extent of rDNA heterochromatin formation. PMID:10388812 Any process that decreases the rate, frequency, or extent of ribosomal DNA heterochromatin formation. https://github.com/geneontology/go-ontology/issues/19238 https://github.com/geneontology/go-ontology/issues/23782 dph 2010-07-14T09:07:59Z negative regulation of chromatin silencing at rDNA negative regulation of ribosomal DNA heterochromatin assembly negative regulation of ribosomal DNA heterochromatin formation biological_process GO:0061188 negative regulation of rDNA heterochromatin formation GO:0061188 Any process that decreases the rate, frequency, or extent of ribosomal DNA heterochromatin formation. GOC:dph PMID:10388812 Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation. dph 2014-05-14T15:36:53Z H3-K27me3 modified histone binding molecular_function GO:0061628 H3K27me3 modified histone binding GO:0061628 Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation. GOC:dph PMID:23948251 H3-K27me3 modified histone binding GOC:dph Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription. https://github.com/geneontology/go-ontology/issues/19354 dph 2014-05-15T09:12:24Z GO:0001085 GO:0001102 GO:0001103 RNA polymerase II sequence-specific DNA binding transcription factor binding RNA polymerase II sequence-specific DNA-binding transcription factor binding molecular_function RNA polymerase II activating transcription factor binding RNA polymerase II repressing transcription factor binding RNA polymerase II transcription factor binding GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding GO:0061629 Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription. GOC:dph GOC:vw The modification of histone H3 at a lysine in position 9 of the histone. dph 2014-10-02T15:07:42Z biological_process GO:0061647 histone H3-K9 modification GO:0061647 The modification of histone H3 at a lysine in position 9 of the histone. GOC:vw Binding to a histone protein in which a residue has been modified by ubiquitination. dph 2014-11-04T10:21:04Z molecular_function ubiquitinated histone binding GO:0061649 ubiquitin modification-dependent histone binding GO:0061649 Binding to a histone protein in which a residue has been modified by ubiquitination. GOC:dph PMID:24526689 A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). dph 2015-05-06T11:22:38Z cellular_component GO:0061695 transferase complex, transferring phosphorus-containing groups GO:0061695 A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:bhm GOC:dph Catalysis of the reaction: acetyl-CoA + lysine in peptide = CoA + N-acetyl-lysine-peptide. dph 2015-09-10T10:22:19Z protein acetylase activity protein acetyltransferase activity RHEA:45948 Reactome:R-HSA-6811508 Reactome:R-HSA-8951966 Reactome:R-HSA-9617758 Reactome:R-HSA-9620515 Reactome:R-HSA-9626945 Reactome:R-HSA-9701531 Reactome:R-HSA-9756494 peptide-lysine-N-acetylase activity protein-lysine-N-acetylase activity molecular_function GO:0061733 peptide-lysine-N-acetyltransferase activity GO:0061733 Catalysis of the reaction: acetyl-CoA + lysine in peptide = CoA + N-acetyl-lysine-peptide. GOC:dph RHEA:45948 Reactome:R-HSA-6811508 ING2-bound EP300 acetylates TP53 Reactome:R-HSA-8951966 EP300 acetylates RUNX3 Reactome:R-HSA-9617758 EP300,CREBBP acetylate FOXO4 Reactome:R-HSA-9620515 KAT2B,EP300 acetylate FOXO3 under oxidative stress Reactome:R-HSA-9626945 CREBBP acetylates FOXO1 Reactome:R-HSA-9701531 p-Y705,S727 STAT3 is acetylated Reactome:R-HSA-9756494 CREBBP acetylates SARS-CoV-2 N at K375 A chromatin silencing complex that recruits histone-modifying enzymes and upregulates silencing of rDNA in response to glucose starvation. dph 2016-07-09T10:12:30Z energy dependent nucleolar silencing complex cellular_component GO:0061773 eNoSc complex GO:0061773 A chromatin silencing complex that recruits histone-modifying enzymes and upregulates silencing of rDNA in response to glucose starvation. GOC:BHM Intact:EBI-11789632 Intact:EBI-11790279 PMID:18485871 A chromatin silencing complex that binds and bridges separate nucleosomal histones resulting in heterochromatin assembly and chromatin looping. dph 2016-09-09T13:47:27Z cellular_component nucleosome bridging complex GO:0061793 chromatin lock complex GO:0061793 A chromatin silencing complex that binds and bridges separate nucleosomal histones resulting in heterochromatin assembly and chromatin looping. GOC:bhm GOC:dph PMID:17540172 nucleosome bridging complex GOC:dph Binding to a NuA4 histone acetyltransferase complex. dph 2018-08-31T13:51:45Z molecular_function GO:0062060 NuA4 histone acetyltransferase complex binding GO:0062060 Binding to a NuA4 histone acetyltransferase complex. PMID:15528408 Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation. dph 2018-09-05T12:58:43Z molecular_function GO:0062072 H3K9me3 modified histone binding GO:0062072 Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation. PMID:30110338 Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation GO:0065007 Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function GO:0065009 Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete The modification of a histone by the removal of a methyl group from a lysine residue. biological_process GO:0070076 histone lysine demethylation GO:0070076 The modification of a histone by the removal of a methyl group from a lysine residue. GOC:mah The modification of histone H3 by the removal of a methyl group from arginine at position 2 of the histone. biological_process GO:0070078 histone H3-R2 demethylation GO:0070078 The modification of histone H3 by the removal of a methyl group from arginine at position 2 of the histone. GOC:BHF GOC:vk The modification of histone H4 by the removal of a methyl group from arginine at position 3 of the histone. biological_process GO:0070079 histone H4-R3 demethylation GO:0070079 The modification of histone H4 by the removal of a methyl group from arginine at position 3 of the histone. GOC:BHF GOC:vk A process of chromosome organization that is involved in a meiotic cell cycle. chromosome organisation involved in meiosis meiotic chromosome organization biological_process GO:0070192 chromosome organization involved in meiotic cell cycle GO:0070192 A process of chromosome organization that is involved in a meiotic cell cycle. GOC:mah chromosome organisation involved in meiosis GOC:mah meiotic chromosome organization GOC:mah Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome. protein localisation to chromosome, telomeric region protein localization to telomere biological_process GO:0070198 protein localization to chromosome, telomeric region GO:0070198 Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome. GOC:BHF GOC:mah protein localisation to chromosome, telomeric region GOC:mah protein localization to telomere GOC:mah The directed movement of a protein to a specific location on a chromosome. establishment of protein localisation to chromosome biological_process GO:0070199 establishment of protein localization to chromosome GO:0070199 The directed movement of a protein to a specific location on a chromosome. GOC:BHF GOC:mah establishment of protein localisation to chromosome GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process GO:0070201 regulation of establishment of protein localization GO:0070201 Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah A protein complex that is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and the DNA end-binding heterodimer Ku. DNA-PK complex DNA-PK-Ku antigen complex DNA-dependent protein kinase, DNA-end-binding complex cellular_component GO:0070418 DNA-dependent protein kinase complex GO:0070418 A protein complex that is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and the DNA end-binding heterodimer Ku. GOC:mah PMID:10854421 PMID:12235392 DNA-PK-Ku antigen complex CORUM:355 A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends. NHEJ complex non-homologous end joining complex cellular_component GO:0070419 nonhomologous end joining complex GO:0070419 A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends. GOC:mah PMID:17072889 PMID:17938628 NHEJ complex GOC:mah non-homologous end joining complex GOC:mah A histone acetyltransferase complex that acetylates nucleosomal histones H2B, H3, or H4 and is required for the expression of a subset of Pol II-transcribed genes. This complex includes the acetyltransferases GCN5/KAT2A or PCAF/KAT2B, several proteins of the ADA, SGF and SPT families, and several TBP-associate proteins (TAFs). SAGA family complex cellular_component GO:0070461 SAGA-type complex GO:0070461 A histone acetyltransferase complex that acetylates nucleosomal histones H2B, H3, or H4 and is required for the expression of a subset of Pol II-transcribed genes. This complex includes the acetyltransferases GCN5/KAT2A or PCAF/KAT2B, several proteins of the ADA, SGF and SPT families, and several TBP-associate proteins (TAFs). GOC:mah PMID:10637607 PMID:17337012 SAGA family complex PMID:17337012 A protein complex that contains the BRCA1-BARD1 heterodimer, CtIP and Mre11/Rad50/NBS1 (M/R/N) complex, and binds to DNA at DNA damage sites. BRCA1-C binding ta damaged DNA is required for DNA damage-induced Chk1 phosphorylation and the G2/M transition checkpoint. cellular_component GO:0070533 BRCA1-C complex GO:0070533 A protein complex that contains the BRCA1-BARD1 heterodimer, CtIP and Mre11/Rad50/NBS1 (M/R/N) complex, and binds to DNA at DNA damage sites. BRCA1-C binding ta damaged DNA is required for DNA damage-induced Chk1 phosphorylation and the G2/M transition checkpoint. GOC:mah PMID:15485915 PMID:16391231 Binding to a histone in which a lysine residue has been modified by acetylation. mah 2009-04-21T03:03:35Z acetylated histone residue binding molecular_function GO:0070577 lysine-acetylated histone binding GO:0070577 Binding to a histone in which a lysine residue has been modified by acetylation. GOC:BHF GOC:mah GOC:rl PMID:17582821 acetylated histone residue binding GOC:rl A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the catalytic subunit components (ATPase) and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP. mah 2009-04-29T12:55:46Z GO:0090544 BAF-type complex SWI-SNF-type complex cellular_component SWI-SNF global transcription activator complex SWI/SNF-type complex SWI2/SNF2 superfamily ATP-dependent chromatin remodeling complex GO:0070603 SWI/SNF superfamily-type complex GO:0070603 A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the catalytic subunit components (ATPase) and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP. GOC:bhm GOC:krc GOC:mah PMID:16155938 SWI-SNF-type complex GOC:mah SWI-SNF global transcription activator complex CORUM:224 SWI/SNF-type complex GOC:krc SWI2/SNF2 superfamily ATP-dependent chromatin remodeling complex GOC:krc true Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 2) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 2). This reaction is the addition of a methyl group to the arginine residue at position 2 of histone H3. mah 2009-04-29T02:04:44Z histone H3R2 arginine methyltransferase activity histone methylase activity (H3-R2 specific) histone methyltransferase activity (H3-R2 specific) histone-H3R2 methyltransferase activity histone-arginine N-methyltransferase activity (H3-R2 specific) molecular_function GO:0070611 histone H3R2 methyltransferase activity GO:0070611 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 2) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 2). This reaction is the addition of a methyl group to the arginine residue at position 2 of histone H3. GOC:mah PMID:17898714 histone methylase activity (H3-R2 specific) GOC:mah histone-arginine N-methyltransferase activity (H3-R2 specific) GOC:mah Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H2A)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H2A. mah 2009-04-29T02:06:45Z histone H2AR3 arginine methyltransferase activity histone methylase activity (H2A-R3 specific) histone methyltransferase activity (H2A-R3 specific) histone-H2AR3 methyltransferase activity histone-arginine N-methyltransferase activity (H2A-R3 specific) molecular_function GO:0070612 histone H2AR3 methyltransferase activity GO:0070612 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H2A)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H2A. GOC:mah PMID:17898714 PMID:23451136 histone H2AR3 arginine methyltransferase activity GOC:mah histone methylase activity (H2A-R3 specific) GOC:mah histone-arginine N-methyltransferase activity (H2A-R3 specific) GOC:mah A protein modification process in which one or more covalently attached groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are removed from a target protein. mah 2009-05-11T01:58:15Z biological_process GO:0070646 protein modification by small protein removal GO:0070646 A protein modification process in which one or more covalently attached groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are removed from a target protein. GOC:mah A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein. mah 2009-05-11T02:54:03Z biological_process GO:0070647 protein modification by small protein conjugation or removal GO:0070647 A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein. GOC:mah Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization GO:0070727 Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone. mah 2009-06-19T11:44:37Z histone H3 K27 methylation histone H3K27me histone lysine H3 K27 methylation biological_process GO:0070734 histone H3-K27 methylation GO:0070734 The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone. GOC:mah GOC:pr histone H3 K27 methylation GOC:mah histone H3K27me GOC:mah histone lysine H3 K27 methylation GOC:mah A multisubunit complex that catalyzes the acetylation of histone H3. mah 2009-07-02T11:56:48Z H3 HAT complex cellular_component GO:0070775 H3 histone acetyltransferase complex GO:0070775 A multisubunit complex that catalyzes the acetylation of histone H3. GOC:mah H3 HAT complex GOC:mah A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3. mah 2009-07-02T12:06:04Z cellular_component GO:0070776 MOZ/MORF histone acetyltransferase complex GO:0070776 A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3. PMID:18794358 Any of a number of evolutionarily conserved histone deacetylase complexes (HDACs) containing a core consisting of a paired amphipathic helix motif protein (e.g. Sin3p in S. cerevisiae, Pst1 in S. pombe or Sin3A in mammals) at least one class I histone deacetylase (e.g. Rpd3p in S. cerevisiae, Clr6 in S. pombe, or HDAC1 and HDAC2 in mammals), and at least one WD40 repeat protein (e.g. Ume1p in S. cerevisiae, Prw1 in S. pombe, or RbAp46 and RbAp48 in mammals). These complexes also contain a variable number of other proteins that direct histone binding, DNA binding, or add other functionality to the complex. mah 2009-07-20T04:32:33Z cellular_component GO:0070822 Sin3-type complex GO:0070822 Any of a number of evolutionarily conserved histone deacetylase complexes (HDACs) containing a core consisting of a paired amphipathic helix motif protein (e.g. Sin3p in S. cerevisiae, Pst1 in S. pombe or Sin3A in mammals) at least one class I histone deacetylase (e.g. Rpd3p in S. cerevisiae, Clr6 in S. pombe, or HDAC1 and HDAC2 in mammals), and at least one WD40 repeat protein (e.g. Ume1p in S. cerevisiae, Prw1 in S. pombe, or RbAp46 and RbAp48 in mammals). These complexes also contain a variable number of other proteins that direct histone binding, DNA binding, or add other functionality to the complex. PMID:15565322 PMID:18292778 Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin. mah 2009-07-23T04:12:48Z heterochromatin organisation biological_process GO:0070828 heterochromatin organization GO:0070828 Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin. GOC:mah heterochromatin organisation GOC:mah The modification of histone H3 by the removal of one or more acetyl groups. mah 2009-09-16T04:50:55Z biological_process GO:0070932 histone H3 deacetylation GO:0070932 The modification of histone H3 by the removal of one or more acetyl groups. GOC:BHF GOC:rl The modification of histone H4 by the removal of one or more acetyl groups. mah 2009-09-16T04:53:06Z biological_process GO:0070933 histone H4 deacetylation GO:0070933 The modification of histone H4 by the removal of one or more acetyl groups. GOC:BHF GOC:rl The process of removing one or more methyl groups from a molecule. mah 2009-10-29T03:12:51Z biological_process GO:0070988 demethylation GO:0070988 The process of removing one or more methyl groups from a molecule. GOC:BHF GOC:rl Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin. mah 2009-11-20T11:51:20Z protein localisation to chromatin biological_process GO:0071168 protein localization to chromatin GO:0071168 Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin. GOC:mah protein localisation to chromatin GOC:mah The directed movement of a protein to a part of a chromosome that is organized into chromatin. mah 2009-11-20T11:52:43Z establishment of protein localisation to chromatin biological_process GO:0071169 establishment of protein localization to chromatin GO:0071169 The directed movement of a protein to a part of a chromosome that is organized into chromatin. GOC:mah establishment of protein localisation to chromatin GOC:mah A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5. mah 2009-12-11T11:11:36Z cellular_component GO:0071339 MLL1 complex GO:0071339 A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5. GOC:sp PMID:15960975 Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome. mah 2009-12-17T02:11:23Z protein localisation to chromosome, centromeric region protein localization to centromere protein localization to chromosome, centric region biological_process GO:0071459 protein localization to chromosome, centromeric region GO:0071459 Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome. GOC:mah protein localisation to chromosome, centromeric region GOC:mah protein localization to centromere GOC:mah protein localization to chromosome, centric region GOC:mah The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone. mah 2010-01-15T10:59:50Z biological_process H3K27 demethylation GO:0071557 histone H3-K27 demethylation GO:0071557 The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone. GOC:sp PMID:20023638 H3K27 demethylation GOC:mah Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 27 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. mah 2010-01-15T11:33:17Z histone demethylase activity (H3-K27 specific) EC:1.14.11.68 RHEA:60224 Reactome:R-HSA-3222593 Reactome:R-HSA-5617431 Reactome:R-HSA-5617887 histone H3-tri/di-methyl-lysine-27 demethylase activity molecular_function histone H3K27me2 demethylase activity histone H3K27me3 demethylase activity GO:0071558 histone H3K27me2/H3K27me3 demethylase activity GO:0071558 Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 27 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. GOC:sp PMID:20622853 Reactome:R-HSA-3222593 KDM6B demethylates H3K27me3 on p16INK4A promoter Reactome:R-HSA-5617431 Retinoic acid activates HOXA1 chromatin Reactome:R-HSA-5617887 HOXC4 chromatin is activated A SWI/SNF-type complex that is found in neural stem or progenitor cells, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A genes. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. mah 2010-01-20T03:33:42Z cellular_component GO:0071564 npBAF complex GO:0071564 A SWI/SNF-type complex that is found in neural stem or progenitor cells, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A genes. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. GOC:mah GOC:ss PMID:17640523 A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. mah 2010-01-20T03:41:19Z cellular_component GO:0071565 nBAF complex GO:0071565 A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. GOC:mah GOC:ss PMID:17640523 The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. mah 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport GO:0071702 The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process GO:0071704 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. mah 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The aggregation, arrangement and bonding together of a set of components to form a membrane. mah 2010-03-10T11:19:17Z biological_process GO:0071709 membrane assembly GO:0071709 The aggregation, arrangement and bonding together of a set of components to form a membrane. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. mah 2010-03-29T03:59:35Z nuclear membrane organisation biological_process nuclear membrane organization and biogenesis GO:0071763 nuclear membrane organization GO:0071763 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. GOC:mah nuclear membrane organisation GOC:mah nuclear membrane organization and biogenesis GOC:mah Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex. mah 2010-09-08T10:03:26Z DNA-protein complex subunit organization protein-DNA complex subunit organisation protein-DNA complex subunit organization biological_process GO:0071824 protein-DNA complex organization GO:0071824 Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex. GOC:mah DNA-protein complex subunit organization GOC:mah protein-DNA complex subunit organisation GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis GO:0071840 A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residue at position 16. In human, it contains the catalytic subunit MOF, and MSL1, MSL2 and MSL3. mah 2010-12-10T10:15:11Z cellular_component GO:0072487 MSL complex GO:0072487 A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residue at position 16. In human, it contains the catalytic subunit MOF, and MSL1, MSL2 and MSL3. PMID:16227571 PMID:20018852 The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. mah 2011-02-14T01:56:51Z establishment of protein localisation to organelle biological_process GO:0072594 establishment of protein localization to organelle GO:0072594 The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. GOC:mah establishment of protein localisation to organelle GOC:mah Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. mah 2011-02-14T02:09:13Z maintenance of protein localisation to organelle maintenance of protein localization to organelle biological_process GO:0072595 maintenance of protein localization in organelle GO:0072595 Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. GOC:mah maintenance of protein localisation to organelle GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. dhl 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process GO:0080090 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone. dhl 2011-08-10T04:18:36Z biological_process GO:0080182 histone H3-K4 trimethylation GO:0080182 The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone. GOC:BHF GOC:se GOC:tb Any process that activates or increases the frequency, rate or extent of deacetylase activity, the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. tb 2009-08-03T12:00:14Z biological_process GO:0090045 positive regulation of deacetylase activity GO:0090045 Any process that activates or increases the frequency, rate or extent of deacetylase activity, the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-09-09T11:39:52Z biological_process GO:0090068 positive regulation of cell cycle process GO:0090068 Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any cellular metabolic process involving nucleic acids. tb 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process GO:0090304 Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation. https://github.com/geneontology/go-ontology/issues/23553 tb 2010-04-09T02:12:53Z regulation of methylation-dependent chromatin silencing regulation of DNA methylation-dependent heterochromatin assembly biological_process GO:0090308 regulation of DNA methylation-dependent heterochromatin formation GO:0090308 Any process that modulates the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation. GOC:BHF Any process that increases the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation. https://github.com/geneontology/go-ontology/issues/23553 tb 2010-04-09T02:12:53Z positive regulation of methylation-dependent chromatin silencing positive regulation of DNA methylation-dependent heterochromatin assembly biological_process GO:0090309 positive regulation of DNA methylation-dependent heterochromatin formation GO:0090309 Any process that increases the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation. GOC:BHF Any process that modulates the rate, frequency, or extent of protein deacetylation, the removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. tb 2010-04-14T01:30:45Z regulation of protein amino acid deacetylation biological_process GO:0090311 regulation of protein deacetylation GO:0090311 Any process that modulates the rate, frequency, or extent of protein deacetylation, the removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. GOC:tb regulation of protein amino acid deacetylation GOC:bf Any process that increases the rate, frequency, or extent of protein deacetylation, the removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. tb 2010-04-14T01:30:45Z positive regulation of protein amino acid deacetylation biological_process GO:0090312 positive regulation of protein deacetylation GO:0090312 Any process that increases the rate, frequency, or extent of protein deacetylation, the removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. GOC:ecd PMID:20027304 positive regulation of protein amino acid deacetylation GOC:bf Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090316 positive regulation of intracellular protein transport GO:0090316 Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090317 negative regulation of intracellular protein transport GO:0090317 Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that modulates the rate, frequency, or extent of DNA-templated DNA replication, the process in which new strands of DNA are synthesized. tb 2010-05-14T10:42:04Z regulation of DNA-dependent DNA replication biological_process GO:0090329 regulation of DNA-templated DNA replication GO:0090329 Any process that modulates the rate, frequency, or extent of DNA-templated DNA replication, the process in which new strands of DNA are synthesized. GOC:dph GOC:tb An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and WSTF (Williams Syndrome Transcription Factor). WICH plays roles in regulation of RNAP I and III transcription and in DNA replication and repair. tb 2013-02-11T14:07:14Z cellular_component GO:0090535 WICH complex GO:0090535 An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and WSTF (Williams Syndrome Transcription Factor). WICH plays roles in regulation of RNAP I and III transcription and in DNA replication and repair. GOC:krc PMID:15284901 PMID:16568949 PMID:21810179 An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and a Tip5 homolog. In mammals, NoRC is involved in regulation of transcription from RNAP I and RNA polymerase III promoters. tb 2013-02-11T14:07:14Z cellular_component GO:0090536 NoRC complex GO:0090536 An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2H in mammals, which contain two ISWI homologs) and a Tip5 homolog. In mammals, NoRC is involved in regulation of transcription from RNAP I and RNA polymerase III promoters. GOC:krc An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2L in mammals, which contain two ISWI homologs) and a CECR2 homolog. In mammals, CERF is involved in regulation of transcription from RNA polymerase II promoters. tb 2013-02-11T14:07:14Z cellular_component GO:0090537 CERF complex GO:0090537 An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2L in mammals, which contain two ISWI homologs) and a CECR2 homolog. In mammals, CERF is involved in regulation of transcription from RNA polymerase II promoters. GOC:krc A SWI/SNF-type complex that contains a subunit from the CHD(Chromodomain helicase DNA-binding) family. The CHD family is characterized by two signature sequence motifs: tandem chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein structure. tb 2013-02-15T12:11:57Z cellular_component GO:0090545 CHD-type complex GO:0090545 A SWI/SNF-type complex that contains a subunit from the CHD(Chromodomain helicase DNA-binding) family. The CHD family is characterized by two signature sequence motifs: tandem chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein structure. GOC:krc GOC:tb PMID:17350655 true A transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase II. tb 2014-05-09T14:04:37Z RNA polymerase II transcription factor complex cellular_component GO:0090575 RNA polymerase II transcription regulator complex GO:0090575 A transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase II. GOC:tb A transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase III. tb 2014-05-09T14:04:37Z RNA polymerase III transcription factor complex cellular_component GO:0090576 RNA polymerase III transcription regulator complex GO:0090576 A transcription factor complex that acts at a regulatory region of a gene transcribed by RNA polymerase III. GOC:tb Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. pr 2011-09-23T02:31:01Z molecular_function GO:0097159 organic cyclic compound binding GO:0097159 Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. GOC:sjw PMID:7583672 A heterodimeric protein complex that contains a protease inhibitor and a protease; formation of the complex inhibits protease activity. pr 2011-10-16T08:53:44Z peptidase inhibitor complex cellular_component GO:0097179 protease inhibitor complex GO:0097179 A heterodimeric protein complex that contains a protease inhibitor and a protease; formation of the complex inhibits protease activity. GOC:ans PMID:6323392 A heterodimeric protein complex that contains a serine protease inhibitor and a protease; formation of the complex inhibits serine protease activity. pr 2011-10-16T08:55:17Z serine-type endopeptidase inhibitor complex serpin complex cellular_component GO:0097180 serine protease inhibitor complex GO:0097180 A heterodimeric protein complex that contains a serine protease inhibitor and a protease; formation of the complex inhibits serine protease activity. GOC:ans PMID:6323392 serine-type endopeptidase inhibitor complex GOC:bf GOC:pr The modification of histone H3 by addition of three methyl groups to lysine at position 36 of the histone. pr 2011-12-05T01:19:45Z biological_process GO:0097198 histone H3-K36 trimethylation GO:0097198 The modification of histone H3 by addition of three methyl groups to lysine at position 36 of the histone. GOC:se PMID:17948059 A chromatin remodeling protein complex initially purified from S. cerevisiae and containing more than 10 subunits, including the SWR1-related complexes. INO80 (inositol requiring 80)-type complexes have diverse functions, including promoting transcriptional activation and DNA repair. pr 2012-06-20T11:26:55Z cellular_component GO:0097346 INO80-type complex GO:0097346 A chromatin remodeling protein complex initially purified from S. cerevisiae and containing more than 10 subunits, including the SWR1-related complexes. INO80 (inositol requiring 80)-type complexes have diverse functions, including promoting transcriptional activation and DNA repair. GOC:rb PMID:19355820 Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin. pr 2012-07-03T03:19:07Z protein localisation to heterochromatin biological_process GO:0097355 protein localization to heterochromatin GO:0097355 Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin. GOC:mah protein localisation to heterochromatin GOC:mah Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 18) + H2O = histone H3 L-lysine (position 18) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 18 of the histone H3 protein. pr 2012-09-05T13:16:39Z NAD-dependent histone H3-K18 deacetylase activity NAD-dependent histone deacetylase activity (H3-K18 specific) molecular_function GO:0097372 NAD-dependent histone H3K18 deacetylase activity GO:0097372 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 18) + H2O = histone H3 L-lysine (position 18) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 18 of the histone H3 protein. GOC:sp PMID:22722849 PMID:28450737 A protein-DNA complex consisting of a higher-order oligomer of strand exchange proteins (recombinases) on single-stranded DNA. pr 2013-10-16T15:43:22Z cellular_component GO:0097519 DNA recombinase complex GO:0097519 A protein-DNA complex consisting of a higher-order oligomer of strand exchange proteins (recombinases) on single-stranded DNA. GOC:cjm PMID:10357855 A small ribonucleoprotein complex involved in formation of the spliceosome. pr 2013-10-18T15:57:45Z cellular_component GO:0097525 spliceosomal snRNP complex GO:0097525 A small ribonucleoprotein complex involved in formation of the spliceosome. GOC:krc GOC:pr ISBN:0879695897 A spliceosomal snRNP complex that is formed by the association of the U4/U6 (or U4atac/U6atac) snRNP with the U5 snRNP. pr 2013-10-18T15:58:47Z cellular_component GO:0097526 spliceosomal tri-snRNP complex GO:0097526 A spliceosomal snRNP complex that is formed by the association of the U4/U6 (or U4atac/U6atac) snRNP with the U5 snRNP. GOC:krc GOC:pr ISBN:0879695897 PMID:9452384 A protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription. pr 2014-01-22T09:33:44Z DNA-templated transcriptional preinitiation complex transcriptional pre-initiation complex transcriptional preinitiation complex PIC preinitiation complex cellular_component GO:0097550 transcription preinitiation complex GO:0097550 A protein-DNA complex composed of proteins binding promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription. GOC:di PMID:22751016 A phosphatidylinositol 3-kinase complex that contains a catalytic and a regulatory subunit of a phosphatidylinositol 3-kinase (PI3K) enzyme, plus one or more adaptor proteins. Class I PI3Ks phosphorylate phosphatidylinositol [PI], phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], and are divided into subclasses A and B according to the type of adaptor subunit with which they associate. The class I PI3K subfamily of genes comprises members in vertebrates, worm and fly, but none in yeast. pr 2014-09-16T11:19:58Z class I PI3K complex class I phosphatidylinositol 3-kinase complex cellular_component GO:0097651 phosphatidylinositol 3-kinase complex, class I GO:0097651 A phosphatidylinositol 3-kinase complex that contains a catalytic and a regulatory subunit of a phosphatidylinositol 3-kinase (PI3K) enzyme, plus one or more adaptor proteins. Class I PI3Ks phosphorylate phosphatidylinositol [PI], phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], and are divided into subclasses A and B according to the type of adaptor subunit with which they associate. The class I PI3K subfamily of genes comprises members in vertebrates, worm and fly, but none in yeast. GOC:ha PMID:24587488 The modification of histone H3 by addition of two methyl groups to lysine at position 36 of the histone. pr 2014-11-04T10:38:05Z biological_process GO:0097676 histone H3-K36 dimethylation GO:0097676 The modification of histone H3 by addition of two methyl groups to lysine at position 36 of the histone. GOC:lb PMID:21187428 The modification of histone H3 by addition of three methyl groups to lysine at position 27 of the histone. dos 2013-10-18T14:11:17Z biological_process GO:0098532 histone H3-K27 trimethylation GO:0098532 The modification of histone H3 by addition of three methyl groups to lysine at position 27 of the histone. PMID:19270745 Any subdivision of a chromosome along its length. chromosome region cellular_component GO:0098687 Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. chromosomal region GO:0098687 Any subdivision of a chromosome along its length. GOC:dos The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a macromolecule. biological_process GO:0098732 macromolecule deacylation GO:0098732 The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a macromolecule. GOC:dos A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition. https://github.com/geneontology/go-ontology/issues/20854 https://github.com/geneontology/go-ontology/issues/20862 https://github.com/geneontology/go-ontology/issues/25165 molecular function regulator molecular_function GO:0098772 molecular function regulator activity GO:0098772 A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition. GOC:dos GOC:pt Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex GO:0098796 Any protein complex that is part of a membrane. GOC:dos Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex GO:0098797 Any protein complex that is part of the plasma membrane. GOC:dos A region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes. This region is usually heterochromatin. https://github.com/geneontology/go-ontology/issues/19086 https://github.com/geneontology/go-ontology/issues/22353 vw 2014-07-18T13:32:59Z GO:1990421 GO:1990707 SO:0001997 subtelomere nuclear subtelomeric heterochromatin cellular_component sub-telomeric heterochromatin subtelomeric heterochromatin GO:0099115 chromosome, subtelomeric region GO:0099115 A region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes. This region is usually heterochromatin. GOC:mah PMID:18761674 PMID:22771823 PMID:26205977 PMID:7660126 A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis. https://github.com/geneontology/go-ontology/issues/19949 nuclear membrane organization involved in mitotic nuclear division biological_process GO:0101024 This process only occurs in organisms which undergo 'closed mitosis' without nuclear breakdown. mitotic nuclear membrane organization GO:0101024 A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis. GOC:vw PMID:15147872 Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: succinyl-CoA + peptide = CoA + N-succinylpeptide. hjd 2017-12-15T18:23:58Z molecular_function GO:0106075 peptide N-succinyltransferase activity GO:0106075 Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: succinyl-CoA + peptide = CoA + N-succinylpeptide. PMID:29211711 The modification of a histone by the addition of an succinyl group. hjd 2017-12-15T18:27:16Z biological_process GO:0106077 histone succinylation GO:0106077 The modification of a histone by the addition of an succinyl group. PMID:29211711 Catalysis of the reaction: succinyl-CoA + histone = CoA + succinyl-histone. hjd 2017-12-15T18:29:40Z molecular_function GO:0106078 histone succinyltransferase activity GO:0106078 Catalysis of the reaction: succinyl-CoA + histone = CoA + succinyl-histone. PMID:29211711 Catalysis of the reaction: glutaryl-CoA + L-lysyl-[protein] = CoA + H+ + N6-glutaryl-L-lysyl-[protein]. hjd 2019-10-17T18:58:56Z RHEA:18009 molecular_function GO:0106228 peptide glutaryltransferase activity GO:0106228 Catalysis of the reaction: glutaryl-CoA + L-lysyl-[protein] = CoA + H+ + N6-glutaryl-L-lysyl-[protein]. GOC:sp PMID:31542297 Catalysis of the reaction: glutaryl-CoA + histone = CoA + H+ + N6-glutaryl-histone. hjd 2019-10-17T19:01:48Z molecular_function GO:0106229 histone glutaryltransferase activity GO:0106229 Catalysis of the reaction: glutaryl-CoA + histone = CoA + H+ + N6-glutaryl-histone. GOC:sp PMID:31542297 A chromatin remodeling complex that positively regulates histone H3 acetylation, in particular H3K9, by recruiting histone acetyltransferases to rDNA gene regions. Located in the nucleolus where it assembles on RNA Polymerase I (Pol I) and possibly on RNA Polymerase III (Pol III) promoter and coding regions during early G1 phase and activates the post-initiation phases of Pol I transcription. May also activate RNA Polymerase II (Pol II) gene transcription. In mammals, B-WICH contains the WICH complex core of BAZ1B and SMARCA5, additional protein subunits and possibly rRNAs. Although it contains several catalytic subunits it is not clear which functions are carried out by the complex itself. kmv 2017-05-26T19:53:53Z cellular_component GO:0110016 An example is BAZ1B (Q9UIG0) in human in PMID:16603771 (by IPI). B-WICH complex GO:0110016 A chromatin remodeling complex that positively regulates histone H3 acetylation, in particular H3K9, by recruiting histone acetyltransferases to rDNA gene regions. Located in the nucleolus where it assembles on RNA Polymerase I (Pol I) and possibly on RNA Polymerase III (Pol III) promoter and coding regions during early G1 phase and activates the post-initiation phases of Pol I transcription. May also activate RNA Polymerase II (Pol II) gene transcription. In mammals, B-WICH contains the WICH complex core of BAZ1B and SMARCA5, additional protein subunits and possibly rRNAs. Although it contains several catalytic subunits it is not clear which functions are carried out by the complex itself. GOC:bhm PMID:16603771 PMID:21559432 PMID:23555303 PMID:26044184 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity GO:0110165 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv A protein complex containing members of the Like-Sm family of proteins, which includes both the Sm proteins and the Lsm proteins, and which generally form hexameric or heptameric ring structures which bind to RNA. While some of these ring complexes may form independently of RNA, many only form in association with their target RNA. In addition to Lsm-family proteins, many of these complexes contain additional protein members. Members of this family of complexes include the snRNPs which comprise the majority of the spliceosome. Others are involved in the 5' to 3' degradation pathways of mRNAs in the cytoplasm and of unspliced transcripts in the nucleus, as well as other diverse roles. https://github.com/geneontology/go-ontology/issues/14411 krc 2017-11-06T18:46:43Z cellular_component GO:0120114 Sm-like protein family complex GO:0120114 A protein complex containing members of the Like-Sm family of proteins, which includes both the Sm proteins and the Lsm proteins, and which generally form hexameric or heptameric ring structures which bind to RNA. While some of these ring complexes may form independently of RNA, many only form in association with their target RNA. In addition to Lsm-family proteins, many of these complexes contain additional protein members. Members of this family of complexes include the snRNPs which comprise the majority of the spliceosome. Others are involved in the 5' to 3' degradation pathways of mRNAs in the cytoplasm and of unspliced transcripts in the nucleus, as well as other diverse roles. GOC:bhm GOC:krc PMID:19121818 PMID:27627834 Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin. https://github.com/geneontology/go-ontology/issues/16012 krc 2018-07-14T00:19:32Z negative regulation of protein localisation to chromatin biological_process GO:0120186 negative regulation of protein localization to chromatin GO:0120186 Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin. PMID:20889714 PMID:29899453 negative regulation of protein localisation to chromatin GOC:krc Any process that activates or increases the frequency, rate or extent of protein localization to chromatin. https://github.com/geneontology/go-ontology/issues/16012 krc 2018-07-14T00:21:28Z positive regulation of protein localisation to chromatin biological_process GO:0120187 positive regulation of protein localization to chromatin GO:0120187 Any process that activates or increases the frequency, rate or extent of protein localization to chromatin. PMID:20889714 PMID:29899453 positive regulation of protein localisation to chromatin GOC:krc Any process that modulates the frequency, rate, extent or location of heterochromatin organization. https://github.com/geneontology/go-ontology/issues/20020 krc 2020-09-29T20:00:04Z biological_process GO:0120261 regulation of heterochromatin organization GO:0120261 Any process that modulates the frequency, rate, extent or location of heterochromatin organization. GOC:krc Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin organization. https://github.com/geneontology/go-ontology/issues/20020 krc 2020-09-29T20:12:30Z down regulation of heterochromatin organization down-regulation of heterochromatin organization downregulation of heterochromatin organization inhibition of heterochromatin organization biological_process GO:0120262 negative regulation of heterochromatin organization GO:0120262 Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin organization. GOC:krc Any process that activates or increases the frequency, rate or extent of heterochromatin organization. https://github.com/geneontology/go-ontology/issues/20020 krc 2020-09-29T20:19:19Z up regulation of heterochromatin organization up-regulation of heterochromatin organization upregulation of heterochromatin organization activation of heterochromatin organization stimulation of heterochromatin organization biological_process GO:0120263 positive regulation of heterochromatin organization GO:0120263 Any process that activates or increases the frequency, rate or extent of heterochromatin organization. GOC:krc Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[protein]. https://github.com/geneontology/go-ontology/issues/20685 krc 2021-01-19T03:35:54Z RHEA:61996 molecular_function GO:0120300 peptide lactyltransferase activity GO:0120300 Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[protein]. GOC:sp PMID:31645732 RHEA:61996 Catalysis of the reaction: (L-lysyl-[histone] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[histone]. https://github.com/geneontology/go-ontology/issues/20685 krc 2021-01-19T03:38:56Z molecular_function GO:0120301 histone lactyltransferase activity GO:0120301 Catalysis of the reaction: (L-lysyl-[histone] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[histone]. GOC:sp PMID:31645732 One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division GO:0140013 One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 Binding to a protein upon post-translation modification of the target protein. pg 2017-05-17T11:50:41Z molecular_function modified protein binding GO:0140030 This term should only be used when the binding is shown to require a post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the modification. It may be that the PTM causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term. modification-dependent protein binding GO:0140030 Binding to a protein upon post-translation modification of the target protein. PMID:26060076 Binding to a protein upon acetylation of the target protein. pg 2017-05-17T15:35:43Z molecular_function GO:0140033 This term should only be used when the binding is shown to require acetylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of acetylation. It may be that the acetylation causes a conformational change that allows binding of the protein to another region; this type of acetylation-dependent protein binding is valid for annotation to this term. acetylation-dependent protein binding GO:0140033 Binding to a protein upon acetylation of the target protein. PMID:26060076 Binding to a protein upon methylation of the target protein. pg 2017-05-17T15:40:02Z molecular_function GO:0140034 This term should only be used when the binding is shown to require methylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of methylation. It may be that the methylation causes a conformational change that allows binding of the protein to another region; this type of methylation-dependent protein binding is valid for annotation to this term. methylation-dependent protein binding GO:0140034 Binding to a protein upon methylation of the target protein. PMID:26060076 Binding to a protein upon modification by a ubiquitin-like protein of the target protein. pg 2017-05-18T06:11:27Z molecular_function GO:0140035 This term should only be used when the binding is shown to require a ubiquitin-like modification in the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of ubiquitin-like modification. It may be that the modification causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term. ubiquitination-like modification-dependent protein binding GO:0140035 Binding to a protein upon modification by a ubiquitin-like protein of the target protein. PMID:26060076 Binding to a protein upon ubiquitination of the target protein. pg 2017-05-18T06:29:14Z molecular_function GO:0140036 This term should only be used when the binding is shown to require ubiquitination of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of ubiquitination. It may be that the ubiquitination causes a conformational change that allows binding of the protein to another region; this type of ubiquitination-dependent protein binding is valid for annotation to this term. ubiquitin-dependent protein binding GO:0140036 Binding to a protein upon ubiquitination of the target protein. PMID:26060076 Catalysis of the reaction: crotonyl-CoA + lysine in peptide = CoA + N-crotonyl-lysine-peptide. pg 2017-07-20T16:40:57Z RHEA:53908 molecular_function protein crotonyltransferase activity GO:0140064 peptide crotonyltransferase activity GO:0140064 Catalysis of the reaction: crotonyl-CoA + lysine in peptide = CoA + N-crotonyl-lysine-peptide. PMID:25818647 Catalysis of the reaction: butyryl-CoA + lysine in peptide = CoA + N-butyryl-lysine-peptide. pg 2017-07-20T16:46:49Z RHEA:53912 molecular_function protein butyryltransferase activity GO:0140065 peptide butyryltransferase activity GO:0140065 Catalysis of the reaction: butyryl-CoA + lysine in peptide = CoA + N-butyryl-lysine-peptide. PMID:27105113 Catalysis of the reaction: crotonyl-CoA + histone = CoA + crotonyl-histone. pg 2017-07-20T16:55:16Z molecular_function GO:0140068 histone crotonyltransferase activity GO:0140068 Catalysis of the reaction: crotonyl-CoA + histone = CoA + crotonyl-histone. PMID:25818647 Catalysis of the reaction: butyryl-CoA + histone = CoA + butyryl-histone. pg 2017-07-20T16:56:33Z molecular_function GO:0140069 histone butyryltransferase activity GO:0140069 Catalysis of the reaction: butyryl-CoA + histone = CoA + butyryl-histone. PMID:27105113 A brain-specific SWI/SNF-type complex that contains eight or nine proteins, including both conserved (core) and nonconserved components; contains the ATPase product of either the SMARCA4/BAF190A/BRG1 gene, the mammalian ortholog of the yeast SNF2 gene, or the SMARCA2/BAF190B/BRM gene, the mammalian ortholog of the Drosophila brm (brahma) gene, or an ortholog of either of these genes. Compared to the neuron-specific nBAF complex (GO:0071565) it does not contain DPF1, DPF3 or SMARCC1 or their orthologs. May contain PB1/BAF180. pg 2017-09-05T09:22:41Z brain-specific BAF complex brain-specific SWI/SNF complex cellular_component GO:0140092 bBAF complex GO:0140092 A brain-specific SWI/SNF-type complex that contains eight or nine proteins, including both conserved (core) and nonconserved components; contains the ATPase product of either the SMARCA4/BAF190A/BRG1 gene, the mammalian ortholog of the yeast SNF2 gene, or the SMARCA2/BAF190B/BRM gene, the mammalian ortholog of the Drosophila brm (brahma) gene, or an ortholog of either of these genes. Compared to the neuron-specific nBAF complex (GO:0071565) it does not contain DPF1, DPF3 or SMARCC1 or their orthologs. May contain PB1/BAF180. GOC:bhm PMID:12368262 PMID:12620226 PMID:15525990 PMID:17640523 PMID:17920018 PMID:8804307 PMID:8895581 Catalytic activity that acts to modify a protein. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-14T10:32:59Z molecular_function GO:0140096 catalytic activity, acting on a protein GO:0140096 Catalytic activity that acts to modify a protein. GOC:molecular_function_refactoring GOC:pdt Catalytic activity that acts to modify DNA. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-14T12:03:51Z molecular_function GO:0140097 catalytic activity, acting on DNA GO:0140097 Catalytic activity that acts to modify DNA. GOC:molecular_function_refactoring GOC:pdt Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location. https://github.com/geneontology/go-ontology/issues/14221 https://github.com/geneontology/go-ontology/issues/20848 pg 2017-09-19T13:10:18Z Reactome:R-HSA-3000074 Reactome:R-HSA-3000120 Reactome:R-HSA-3132759 molecular_function GO:0140104 Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization. molecular carrier activity GO:0140104 Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location. GOC:molecular_function_refactoring GOC:pdt Reactome:R-HSA-3000074 TCN2 binds RCbl in the circulation Reactome:R-HSA-3000120 CBLIF binds RCbl Reactome:R-HSA-3132759 TCN1 binds RCbl A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons. https://github.com/geneontology/go-ontology/issues/13588 https://github.com/geneontology/go-ontology/issues/23609 pg 2017-10-18T07:05:44Z molecular_function GO:0140110 transcription regulator activity GO:0140110 A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons. GOC:pg GOC:txnOH-2018 Wikipedia:Transcription_factor A protein complex that has DNA topoisomerase type I and RNA topoisomerase activities. pg 2018-05-29T10:05:33Z Top3-beta-TDRD3 complex cellular_component GO:0140225 DNA topoisomerase III-beta-TDRD3 complex GO:0140225 A protein complex that has DNA topoisomerase type I and RNA topoisomerase activities. GOC:lnp PMID:23912945 PMID:28176834 Top3-beta-TDRD3 complex GOC:krc A SWI/SNF subcomplex that incorporates two mutually exclusive paralogs, GLTSCR1 (glioma tumor suppressor candidate region gene 1) or GLTSCR1L (GLTSCR1-like), BRD9 (bromodomain-containing 9) and the BAF subunits BAF155, BAF60, SS18, BAF53a, and BRG1/BRM. pg 2018-11-20T09:13:52Z cellular_component GO:0140288 GBAF complex GO:0140288 A SWI/SNF subcomplex that incorporates two mutually exclusive paralogs, GLTSCR1 (glioma tumor suppressor candidate region gene 1) or GLTSCR1L (GLTSCR1-like), BRD9 (bromodomain-containing 9) and the BAF subunits BAF155, BAF60, SS18, BAF53a, and BRG1/BRM. PMID:29374058 Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. https://github.com/geneontology/go-ontology/issues/19354 pg 2018-11-28T12:48:20Z GO:0001107 GO:0033613 GO:0070491 molecular_function activating transcription factor binding repressing transcription factor binding transcription activator binding GO:0140297 DNA-binding transcription factor binding GO:0140297 Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. GOC:txnOH-2018 Catalysis of the removal of a methyl group from a protein. https://github.com/geneontology/go-ontology/issues/19325 pg 2020-04-23T07:39:14Z molecular_function GO:0140457 protein demethylase activity GO:0140457 Catalysis of the removal of a methyl group from a protein. PMID:24498420 PMID:28360925 The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex. https://github.com/geneontology/go-ontology/issues/17064 pg 2020-05-08T12:31:39Z chromatin adaptor chromatin adaptor activity chromatin receptor chromatin-protein adaptor protein-chromatin adaptor activity molecular_function chromatin recruitment GO:0140463 chromatin-protein adaptor activity GO:0140463 The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex. PMID:32277274 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. pg 2020-09-09T05:12:38Z nuclear complex cellular_component GO:0140513 nuclear protein-containing complex GO:0140513 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. GOC:pg A protein complex that is part of an endoplasmic reticulum. https://github.com/geneontology/go-ontology/issues/19952 pg 2020-10-28T12:14:12Z cellular_component GO:0140534 endoplasmic reticulum protein-containing complex GO:0140534 A protein complex that is part of an endoplasmic reticulum. GOC:pg A protein-containing complex located intracellularly. https://github.com/geneontology/go-ontology/issues/19952 pg 2020-10-28T14:40:16Z cellular_component GO:0140535 intracellular protein-containing complex GO:0140535 A protein-containing complex located intracellularly. GOC:pg A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery. https://github.com/geneontology/go-ontology/issues/20551 https://github.com/geneontology/go-ontology/issues/22136 pg 2020-12-11T13:25:49Z epigenetic reader histone reader molecular_function GO:0140566 histone reader activity GO:0140566 A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery. PMID:11498575 PMID:25688442 PMID:31082667 PMID:32260176 PMID:34726351 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 8) = S-adenosyl-L-homocysteine + (histone H3-N-methyl-arginine (position 8). This reaction is the addition of a methyl group to the arginine residue at position 8 of histone H3. https://github.com/geneontology/go-ontology/issues/20037 pg 2021-02-09T14:13:17Z histone H3R8 arginine methylase activity histone H3R8 arginine methyltransferase activity histone methyltransferase activity (H3-R8 specific) histone-H3R8 methyltransferase activity molecular_function GO:0140592 histone H3R8 methyltransferase activity GO:0140592 Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 8) = S-adenosyl-L-homocysteine + (histone H3-N-methyl-arginine (position 8). This reaction is the addition of a methyl group to the arginine residue at position 8 of histone H3. PMID:20708585 PMID:31533925 Binding to and carrying a protein between two different cellular components by moving along with the target protein. https://github.com/geneontology/go-ontology/issues/15917 https://github.com/geneontology/go-ontology/issues/22127 https://github.com/geneontology/go-ontology/issues/22356 pg 2021-02-10T06:16:16Z protein chaperone protein carrier activity molecular_function GO:0140597 protein carrier chaperone GO:0140597 Binding to and carrying a protein between two different cellular components by moving along with the target protein. PMID:7628437 Catalytic activity that acts to modify a nucleic acid. https://github.com/geneontology/go-ontology/issues/21402 pg 2021-05-11T06:31:07Z molecular_function GO:0140640 catalytic activity, acting on a nucleic acid GO:0140640 Catalytic activity that acts to modify a nucleic acid. GOC:pg A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient. https://github.com/geneontology/go-ontology/issues/21612 https://github.com/geneontology/go-ontology/issues/22371 pg 2021-06-15T07:35:06Z ATP hydrolysis-dependent activity ATPase activity ATPase activity, coupled ATPase-dependent activity molecular_function GO:0140657 Note that this term represents a grouping class that includes all proteins that use ATP hydrolysis to drive a reaction; it is not meant to capture the ATP hydrolysis reaction itself. To annotate ATP hydrolysis, please use 'ATP hydrolysis activity ; GO:0016887'. ATP-dependent activity GO:0140657 A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient. PMID:24878343 PMID:25750732 PMID:32933017 PMID:33818025 PMID:33873056 PMID:33988324 An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling. https://github.com/geneontology/go-ontology/issues/21609 https://github.com/geneontology/go-ontology/issues/21786 https://github.com/geneontology/go-ontology/issues/6075 pg 2021-06-15T13:57:18Z GO:0070615 ATP hydrolysis-dependent chromatin remodeler activity ATPase-dependent chromatin remodeler activity molecular_function nucleosome-activated ATPase activity nucleosome-dependent ATPase activity GO:0140658 ATP-dependent chromatin remodeler activity GO:0140658 An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling. PMID:14729263 PMID:19165147 PMID:21862382 PMID:30867599 PMID:34313222 nucleosome-activated ATPase activity GOC:mah A chromatin remodeling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and possibly H4. Shares the histone acetylation (HAT) module of GCN5/PCAF-ADA2-ADA3-SGF29 (or orthologs) with the related SAGA complex (GO:0000124). Contains HAT subunits GCN5 or PCAF in a mutually exclusive manner. In addition to the HAT module contains DR1/NC2B, KAT14, MBIP, WDR5, YEATS2 and ZZZ3 or orthologs. Also regulates the activity of non-histone targets and orchestrates mitotic progression by regulating Cyclin A degradation through acetylation. https://github.com/geneontology/go-ontology/issues/21335 pg 2021-06-25T11:05:14Z ADA2A-containing complex Ada Two-A containing complex Ada two A containing complex Ada-Two-A-containing complex G-ATAC complex KAT2A-containing ATAC complex KAT2B-containing ATAC complex cellular_component GO:0140672 ATAC complex GO:0140672 A chromatin remodeling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and possibly H4. Shares the histone acetylation (HAT) module of GCN5/PCAF-ADA2-ADA3-SGF29 (or orthologs) with the related SAGA complex (GO:0000124). Contains HAT subunits GCN5 or PCAF in a mutually exclusive manner. In addition to the HAT module contains DR1/NC2B, KAT14, MBIP, WDR5, YEATS2 and ZZZ3 or orthologs. Also regulates the activity of non-histone targets and orchestrates mitotic progression by regulating Cyclin A degradation through acetylation. GOC:bhm PMID:19936620 PMID:20562830 PMID:28966424 Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 pg 2021-07-08T14:12:22Z histone H3K36me2 demethylase activity EC:1.14.11.27 MetaCyc:RXN-8661 RHEA:42032 histone H3-di/monomethyl-lysine-36 demethylase activity molecular_function histone H3K36me demethylase activity GO:0140680 histone H3K36me/H3K36me2 demethylase activity GO:0140680 Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:20531378 Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 pg 2021-07-08T14:12:31Z histone H3K36me2 demethylase activity EC:1.14.11.69 MetaCyc:RXN-8660 RHEA:60236 histone H3-tri/dimethyl-lysine-36 demethylase activity molecular_function histone H3K36me3 demethylase activity GO:0140681 histone H3K36me2/H3K36me3 demethylase activity GO:0140681 Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:21914792 Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 pg 2021-07-09T06:03:06Z histone H3K9me demethylase activity histone H3K9me2 demethylase activity EC:1.14.11.65 RHEA:60188 histone H3-di/monomethyl-lysine-9 demethylase activity molecular_function GO:0140683 histone H3K9me/H3K9me2 demethylase activity GO:0140683 Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:16603238 Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/21089 pg 2021-07-09T06:03:55Z histone H3K9me2 demethylase activity EC:1.14.11.66 RHEA:60200 histone H3-tri/dimethyl-lysine-9 demethylase activity molecular_function histone H3K9me3 demethylase activity GO:0140684 histone H3K9me2/H3K9me3 demethylase activity GO:0140684 Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:20208542 PMID:20531378 Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome. The histone can be newly synthesized or result from nucleosome disassembly (either spontaneously, or by a histone chaperone). https://github.com/geneontology/go-ontology/issues/22126 https://github.com/geneontology/go-ontology/issues/22129 pg 2021-09-10T15:22:31Z histone carrier activity molecular_function nucleosome remodeling activity GO:0140713 histone chaperone activity GO:0140713 Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome. The histone can be newly synthesized or result from nucleosome disassembly (either spontaneously, or by a histone chaperone). PMID:26459557 The compaction of chromatin into a conformation that is refactory to transcription but that be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression). https://github.com/geneontology/go-ontology/issues/22325 pg 2021-10-29T13:40:47Z fHC assembly facultative heterochromatin assembly biological_process GO:0140718 Note that facultative heterochromatin can be reprogrammed, as opposed to constitutive heterochromatin which usually cannot be reprogrammed to a transcriptionally-competent state. facultative heterochromatin formation GO:0140718 The compaction of chromatin into a conformation that is refactory to transcription but that be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression). PMID:17936700 The compaction of chromatin into a conformation that is refactory to transcription. https://github.com/geneontology/go-ontology/issues/22325 https://github.com/geneontology/go-ontology/issues/23553 pg 2021-10-29T13:41:09Z constitutive heterochromatin assembly biological_process GO:0140719 Note that constitutive heterochromatin indicates that it usually cannot be reprogrammed to a transcriptionally-competent state, as opposed to facultative heterochromatin, which can be reprogrammed. constitutive heterochromatin formation GO:0140719 The compaction of chromatin into a conformation that is refactory to transcription. PMID:17936700 A chromatin remodeler activity that slides core histone octamers along chromosomal DNA. https://github.com/geneontology/go-ontology/issues/22115 pg 2022-01-14T14:53:02Z histone octamer sliding activity molecular_function GO:0140751 This activity is mediated by at least three subfamilies of the SNF2 remodellers, namely the bromodomain domain, the chromodomain containing and the imitation switch subfamilies. histone octamer slider activity GO:0140751 A chromatin remodeler activity that slides core histone octamers along chromosomal DNA. PMID:10466730 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 56) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 56). This reaction is the addition of a methyl group to the lysine residue at position 56 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/22757 https://github.com/geneontology/go-ontology/issues/24337 pg 2022-01-28T08:39:20Z histone H3K56 methylase activity histone lysine N-methyltransferase activity (H3-K56 specific) histone methyltransferase activity (H3-K56 specific) histone-H3K56 methyltransferase activity molecular_function GO:0140759 histone H3K56 methyltransferase activity GO:0140759 Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 56) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 56). This reaction is the addition of a methyl group to the lysine residue at position 56 of the histone H3 protein. PMID:23451023 PMID:28743002 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 56) + H2O = histone H3 L-lysine (position 56) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 56 of the histone H3 protein. https://github.com/geneontology/go-ontology/issues/22829 pg 2022-02-09T08:00:41Z NAD-dependent histone H3-K56 deacetylase activity NAD-dependent histone deacetylase activity (H3-K56 specific) molecular_function GO:0140765 NAD-dependent histone H3K56 deacetylase activity GO:0140765 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 56) + H2O = histone H3 L-lysine (position 56) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 56 of the histone H3 protein. PMID:23911928 PMID:30374165 Catalysis of the reaction: a phosphorylated histone + H2O = a protein + phosphate. https://github.com/geneontology/go-ontology/issues/23148 pg 2022-04-06T08:08:00Z molecular_function GO:0140789 histone phosphatase activity GO:0140789 Catalysis of the reaction: a phosphorylated histone + H2O = a protein + phosphate. PMID:19351884 Catalysis of the reaction: histone H2AX tyrosine phosphate (position 142) + H2O = histone H2AX tyrosine (position 142) + phosphate. https://github.com/geneontology/go-ontology/issues/23148 https://github.com/geneontology/go-ontology/issues/25037 pg 2022-04-06T08:20:40Z histone H2-Y142 phosphatase activity histone tyrosine phosphatase activity (H2-Y142 specific) molecular_function histone H2Y142 phosphatase activity GO:0140793 histone H2AXY142 phosphatase activity GO:0140793 Catalysis of the reaction: histone H2AX tyrosine phosphate (position 142) + H2O = histone H2AX tyrosine (position 142) + phosphate. PMID:19234442 PMID:19351884 Catalysis of the reaction: histone H2AX-tyrosine (position 142) + ATP = (histone H2AX-phosphotyrosine (position 142) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 142 of histone variant H2AX. https://github.com/geneontology/go-ontology/issues/23170 pg 2022-04-08T16:17:40Z gamma-H2AX-S142 kinase activity histone H2AX-Y142 kinase activity histone kinase activity (H2AX-Y142 specific) molecular_function histone H2AY142 kinase activity GO:0140801 histone H2AXY142 kinase activity GO:0140801 Catalysis of the reaction: histone H2AX-tyrosine (position 142) + ATP = (histone H2AX-phosphotyrosine (position 142) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 142 of histone variant H2AX. PMID:19092802 A chromatin remodeling process that allows DNA repair enzyme to access genomic DNA and repair DNA lesions. https://github.com/geneontology/go-ontology/issues/23518 pg 2022-06-21T05:58:39Z DNA damage-dependent chromatin remodeling biological_process GO:0140861 DNA repair-dependent chromatin remodeling GO:0140861 A chromatin remodeling process that allows DNA repair enzyme to access genomic DNA and repair DNA lesions. PMID:15528408 PMID:28053344 PMID:29095668 PMID:35689883 The disruption of nucleosomes during DNA replication to allow the replication machinery to access the DNA. https://github.com/geneontology/go-ontology/issues/23229 pg 2022-07-11T19:41:22Z biological_process GO:0140889 DNA replication-dependent chromatin disassembly GO:0140889 The disruption of nucleosomes during DNA replication to allow the replication machinery to access the DNA. PMID:34471130 PMID:35308047 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 122) = CoA + histone H3 N6-acetyl-L-lysine (position 122). pg 2022-09-09T07:33:35Z histone H3-K122 acetyltransferase activity histone acetylase activity (H3-K122 specific) histone acetyltransferase activity (H3-K122 specific) histone lysine N-acetyltransferase activity (H3-K122 specific) molecular_function GO:0140908 histone H3K122 acetyltransferase activity GO:0140908 Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 122) = CoA + histone H3 N6-acetyl-L-lysine (position 122). PMID:23415232 Catalysis of the reaction: S-adenosyl-L-methionine + a histone H3 = S-adenosyl-L-homocysteine + a methylated histone H3. Histone methylation generally occurs on either an arginine or a lysine residue. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T08:25:30Z histone H3 methylase activity molecular_function histone H3 methylation GO:0140938 histone H3 methyltransferase activity GO:0140938 Catalysis of the reaction: S-adenosyl-L-methionine + a histone H3 = S-adenosyl-L-homocysteine + a methylated histone H3. Histone methylation generally occurs on either an arginine or a lysine residue. PMID:28450737 Catalysis of the reaction: Catalysis of the reaction: S-adenosyl-L-methionine + a histone H4 = S-adenosyl-L-homocysteine + a methylated histone H4. Histone methylation generally occurs on either an arginine or a lysine residue. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T08:29:21Z histone H4 methylase activity histone H4 methylation molecular_function GO:0140939 histone H4 methyltransferase activity GO:0140939 Catalysis of the reaction: Catalysis of the reaction: S-adenosyl-L-methionine + a histone H4 = S-adenosyl-L-homocysteine + a methylated histone H4. Histone methylation generally occurs on either an arginine or a lysine residue. PMID:28450737 Catalysis of the reaction: S-adenosyl-L-methionine + a histone H2 = S-adenosyl-L-homocysteine + a methylated histone H2A. Histone methylation generally occurs on either an arginine or a lysine residue. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T09:07:02Z histone H2A methylase activity molecular_function histone H2A methylation GO:0140940 histone H2A methyltransferase activity GO:0140940 Catalysis of the reaction: S-adenosyl-L-methionine + a histone H2 = S-adenosyl-L-homocysteine + a methylated histone H2A. Histone methylation generally occurs on either an arginine or a lysine residue. PMID:28450737 Catalysis of the reaction: N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H+ + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the monomethlyated lysine residue at position 20 of histone H4, producing H4K20me2. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T09:25:37Z histone H4-K20 dimethylation histone H4K20 dimethylation EC:2.1.1.362 RHEA:60348 histone H4 methyl lysine(20) N-methyltransferase activity (H4-K20 specific) histone H4K20me methylase activity molecular_function GO:0140941 histone H4K20me methyltransferase activity GO:0140941 Catalysis of the reaction: N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H+ + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the monomethlyated lysine residue at position 20 of histone H4, producing H4K20me2. RHEA:60348 Catalysis of the reaction: L-lysyl20-[histone H4] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl20-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 20 of histone H4, producing histone H4K20me. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T09:50:43Z histone H4-K20 methylation histone H4K20 methylase activity histone H4K20 methylation EC:2.1.1.361 RHEA:60344 histone H4K20 monomethylation histone lysine N-monomethyltransferase activity (H4-K20 specific) molecular_function GO:0140944 histone H4K20 monomethyltransferase activity GO:0140944 Catalysis of the reaction: L-lysyl20-[histone H4] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl20-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 20 of histone H4, producing histone H4K20me. RHEA:60344 Catalysis of the reaction: L-lysyl4-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl4-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T09:57:25Z histone H4-K4 methylation histone H4K4 methylation EC:2.1.1.364 RHEA:60264 histone H3K4 monomethylase activity histone lysine N-monomethyltransferase activity (H3-K4 specific) molecular_function GO:0140945 histone H3K4 monomethyltransferase activity GO:0140945 Catalysis of the reaction: L-lysyl4-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl4-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me. RHEA:60264 Catalysis of the reaction: L-lysyl4-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl4-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me2. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T10:01:55Z histone H3-K4 dimethylation histone H3K4 dimethylation EC:2.1.1.370 RHEA:64448 histone H3K4 dimethylase activity histone lysine N-dimethyltransferase activity (H3-K4 specific) molecular_function GO:0140946 histone H3K4 dimethyltransferase activity GO:0140946 Catalysis of the reaction: L-lysyl4-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl4-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me2. RHEA:64448 Catalysis of the reaction: N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the dimethylated lysine residue at position 9 of histone H3, producing histone H3K9me3. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T10:17:34Z histone H3-K9 trimethylation histone H3K9 trimethylation EC:2.1.1.366 RHEA:60280 histone H3K9me2 methylase activity histone dimethyl-lysine(H3K9) N-methyltransferase activity (H3-K9 specific) molecular_function GO:0140947 histone H3K9me2 methyltransferase activity GO:0140947 Catalysis of the reaction: N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the dimethylated lysine residue at position 9 of histone H3, producing histone H3K9me3. RHEA:60280 Catalysis of the reaction: L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T10:21:35Z histone H3-K9 methylation histone H3K9 methylation EC:2.1.1.367 RHEA:60288 histone H3K9 monomethylase activity histone lysine N-monomethyltransferase activity (H3-K9 specific) molecular_function GO:0140948 histone H3K9 monomethyltransferase activity GO:0140948 Catalysis of the reaction: L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me. RHEA:60288 Catalysis of the reaction: L-lysyl9-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me3. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T10:49:29Z histone H3-K9 trimethylation histone H3K9 trimethylation EC:2.1.1.355 RHEA:60276 histone H3K9 mono/di/trimethylase activity histone H3K9 trimethylase activity histone lysine N-trimethyltransferase activity (H3-K9 specific) molecular_function GO:0140949 histone H3K9 trimethyltransferase activity GO:0140949 Catalysis of the reaction: L-lysyl9-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me3. RHEA:60276 Catalysis of the reaction: L-lysyl27-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me3. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T13:26:01Z histone H3-K27 trimethylation histone H3K27 trimethylation EC:2.1.1.356 RHEA:60292 histone H3-K27 trimethylase activity histone H3K27 mono/di/trimethylase activity histone H3K27 trimethylase activity histone lysine N-trimethyltransferase activity (H3-K27 specific) molecular_function GO:0140951 histone H3K27 trimethyltransferase activity GO:0140951 Catalysis of the reaction: L-lysyl27-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me3. RHEA:60292 Catalysis of the reaction: L-lysyl27-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl27-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me2. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T14:44:31Z histone H3-K27 dimethylation histone H3K27 dimethylation EC:2.1.1.371 RHEA:64452 histone H3-K27 dimethylase activity histone H3K27 dimethylase activity histone H3K27 mono/dimethylase activity histone lysine N-dimethyltransferase activity (H3-K27 specific) molecular_function GO:0140952 histone H3K27 dimethyltransferase activity GO:0140952 Catalysis of the reaction: L-lysyl27-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl27-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me2. RHEA:64452 Catalysis of the reaction: L-lysyl36-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me2. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T15:06:50Z histone H3-K36 dimethylation histone H3K36 dimethylation EC:2.1.1.357 RHEA:60308 histone H3K36 dimethylase activity histone H3K36 mono/dimethylase activity histone lysine N-dimethyltransferase activity (H3-K36 specific) molecular_function GO:0140954 histone H3K36 dimethyltransferase activity GO:0140954 Catalysis of the reaction: L-lysyl36-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me2. RHEA:60308 Catalysis of the reaction: L-lysyl36-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me3. https://github.com/geneontology/go-ontology/issues/22588 pg 2022-11-01T15:18:59Z histone H3-K36 trimethylation histone H3K36 trimethylation EC:2.1.1.359 RHEA:60324 histone H3K36 mono/di/trimethylase activity histone H3K36 trimethylase activity histone lysine N-trimethyltransferase activity (H3-K36 specific) molecular_function GO:0140955 histone H3K36 trimethyltransferase activity GO:0140955 Catalysis of the reaction: L-lysyl36-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me3. RHEA:60324 Catalysis of the reaction: L-lysyl79-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl79-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of up to three methyl group to the lysine residue at position 79 of the histone H3 protein, producing H3K79me3. pg 2022-11-01T15:47:14Z histone H3-K79 trimethylation histone H3K79 trimethylation EC:2.1.1.360 RHEA:60328 histone H3K79 trimethylase activity histone lysine N-trimethyltransferase activity (H3-K79 specific) histone trimethylase activity (H3-K79 specific) histone trimethyltransferase activity (H3-K79 specific) histone-H3K79 trimethyltransferase activity molecular_function GO:0140956 histone H3K79 trimethyltransferase activity GO:0140956 Catalysis of the reaction: L-lysyl79-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl79-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of up to three methyl group to the lysine residue at position 79 of the histone H3 protein, producing H3K79me3. PMID:15371351 RHEA:60328 histone trimethylase activity (H3-K79 specific) GOC:mah A catalytic activity that acts on a histone protein. Reversible histone modifications contribute to regulation of gene expression. https://github.com/geneontology/go-ontology/issues/24980 pg 2023-02-22T13:33:01Z molecular_function GO:0140993 histone modifying activity GO:0140993 A catalytic activity that acts on a histone protein. Reversible histone modifications contribute to regulation of gene expression. GOC:pg Catalysis of the reaction: L-lysyl4-[histone H3] + 3 S-adenosyl-L-methionine = 2 H+ + N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me3. https://github.com/geneontology/go-ontology/issues/22588 pg 2023-02-28T12:52:48Z histone H3-K4 trimethylation histone H3K4 trimethylation EC:2.1.1.354 RHEA:60260 histone H3K4 trimethylase activity histone lysine N-trimethyltransferase activity (H3-K4 specific) molecular_function GO:0140999 histone H3K4 trimethyltransferase activity GO:0140999 Catalysis of the reaction: L-lysyl4-[histone H3] + 3 S-adenosyl-L-methionine = 2 H+ + N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me3. PMID:18375658 RHEA:60260 Catalysis of the transfer of a phosphate group to a histone variant H2AX. pg 2023-02-28T13:55:39Z molecular_function GO:0141003 histone H2AX kinase activity GO:0141003 Catalysis of the transfer of a phosphate group to a histone variant H2AX. GOC:bf Catalysis of the reaction: histone H3 N6-acetyl-L-lysine + H2O = histone H3 L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone H3. https://github.com/geneontology/go-ontology/issues/25508 pg 2023-06-07T09:13:49Z molecular_function GO:0141050 histone H3K deacetylase activity GO:0141050 Catalysis of the reaction: histone H3 N6-acetyl-L-lysine + H2O = histone H3 L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone H3. PMID:12590135 Catalysis of the reaction: histone H4 N6-acetyl-L-lysine + H2O = histone H4 L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone H4. https://github.com/geneontology/go-ontology/issues/25508 pg 2023-06-07T09:15:53Z molecular_function GO:0141051 histone H4K deacetylase activity GO:0141051 Catalysis of the reaction: histone H4 N6-acetyl-L-lysine + H2O = histone H4 L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone H4. PMID:12590135 Catalysis of the removal of a methyl group from a modified lysine residue of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/25508 pg 2023-06-07T09:22:57Z molecular_function GO:0141052 histone H3 demethylase activity GO:0141052 Catalysis of the removal of a methyl group from a modified lysine residue of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:17947579 Catalysis of the removal of a methyl group from a modified lysine residue of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. https://github.com/geneontology/go-ontology/issues/25508 pg 2023-06-07T09:47:52Z molecular_function GO:0141058 histone H4 demethylase activity GO:0141058 Catalysis of the removal of a methyl group from a modified lysine residue of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. PMID:17947579 Any process that modulates the frequency, rate or extent of deacetylase activity. bc 2018-07-23T12:24:28Z biological_process GO:0150065 regulation of deacetylase activity GO:0150065 Any process that modulates the frequency, rate or extent of deacetylase activity. GOC:aruk GOC:bc PMID:19457097 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein]. rynl 2021-11-16T00:55:21Z RHEA:69172 molecular_function GO:0160008 protein decrotonylase activity GO:0160008 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein]. PMID:28497810 PMID:30279482 PMID:34608293 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] = (2E)-2-butenoate + L-lysyl-[histone]. rynl 2021-11-16T01:08:57Z molecular_function GO:0160009 histone decrotonylase activity GO:0160009 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] = (2E)-2-butenoate + L-lysyl-[histone]. PMID:28497810 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide. rynl 2021-11-16T01:22:43Z RHEA:69332 molecular_function GO:0160011 NAD-dependent protein decrotonylase activity GO:0160011 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide. PMID:28497810 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[histone] + nicotinamide. rynl 2021-11-16T01:25:28Z molecular_function GO:0160012 NAD-dependent histone decrotonylase activity GO:0160012 Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[histone] + nicotinamide. PMID:28497810 Any process that modulates the frequency, rate or extent of dosage compensation, by inactivation of X chromosome. hjd 2012-02-14T07:29:45Z regulation of chromosome inactivation regulation of X chromosome inactivation biological_process regulation of Barr body formation GO:1900095 regulation of dosage compensation by inactivation of X chromosome GO:1900095 Any process that modulates the frequency, rate or extent of dosage compensation, by inactivation of X chromosome. GOC:TermGenie GOC:mr PMID:20622855 Wikipedia:XY_sex-determination_system regulation of chromosome inactivation GOC:TermGenie regulation of X chromosome inactivation GOC:TermGenie regulation of Barr body formation GOC:TermGenie Any process that modulates the frequency, rate or extent of histone H3-K9 dimethylation. bf 2012-02-21T09:06:18Z regulation of histone H3 K9 dimethylation regulation of histone lysine H3 K9 dimethylation biological_process GO:1900109 regulation of histone H3-K9 dimethylation GO:1900109 Any process that modulates the frequency, rate or extent of histone H3-K9 dimethylation. GOC:TermGenie GOC:vw regulation of histone H3 K9 dimethylation GOC:TermGenie regulation of histone lysine H3 K9 dimethylation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of histone H3-K9 dimethylation. bf 2012-02-21T09:06:26Z positive regulation of histone H3 K9 dimethylation positive regulation of histone lysine H3 K9 dimethylation up regulation of histone H3 K9 dimethylation up regulation of histone H3-K9 dimethylation up regulation of histone lysine H3 K9 dimethylation up-regulation of histone H3 K9 dimethylation up-regulation of histone H3-K9 dimethylation up-regulation of histone lysine H3 K9 dimethylation upregulation of histone H3 K9 dimethylation upregulation of histone H3-K9 dimethylation upregulation of histone lysine H3 K9 dimethylation activation of histone H3 K9 dimethylation activation of histone H3-K9 dimethylation activation of histone lysine H3 K9 dimethylation biological_process GO:1900111 positive regulation of histone H3-K9 dimethylation GO:1900111 Any process that activates or increases the frequency, rate or extent of histone H3-K9 dimethylation. GOC:TermGenie GOC:vw positive regulation of histone H3 K9 dimethylation GOC:TermGenie positive regulation of histone lysine H3 K9 dimethylation GOC:TermGenie up regulation of histone H3 K9 dimethylation GOC:TermGenie up regulation of histone H3-K9 dimethylation GOC:TermGenie up regulation of histone lysine H3 K9 dimethylation GOC:TermGenie up-regulation of histone H3 K9 dimethylation GOC:TermGenie up-regulation of histone H3-K9 dimethylation GOC:TermGenie up-regulation of histone lysine H3 K9 dimethylation GOC:TermGenie upregulation of histone H3 K9 dimethylation GOC:TermGenie upregulation of histone H3-K9 dimethylation GOC:TermGenie upregulation of histone lysine H3 K9 dimethylation GOC:TermGenie activation of histone H3 K9 dimethylation GOC:TermGenie activation of histone H3-K9 dimethylation GOC:TermGenie activation of histone lysine H3 K9 dimethylation GOC:TermGenie Any process that modulates the frequency, rate or extent of histone H3-K9 trimethylation. bf 2012-02-21T09:09:49Z biological_process GO:1900112 regulation of histone H3-K9 trimethylation GO:1900112 Any process that modulates the frequency, rate or extent of histone H3-K9 trimethylation. GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation. bf 2012-02-21T09:09:54Z down regulation of histone H3-K9 trimethylation down-regulation of histone H3-K9 trimethylation downregulation of histone H3-K9 trimethylation inhibition of histone H3-K9 trimethylation biological_process GO:1900113 negative regulation of histone H3-K9 trimethylation GO:1900113 Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation. GOC:TermGenie down regulation of histone H3-K9 trimethylation GOC:TermGenie down-regulation of histone H3-K9 trimethylation GOC:TermGenie downregulation of histone H3-K9 trimethylation GOC:TermGenie inhibition of histone H3-K9 trimethylation GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:44Z regulation of protein localisation to nucleus regulation of protein localization in cell nucleus regulation of protein localization in nucleus biological_process GO:1900180 regulation of protein localization to nucleus GO:1900180 Any process that modulates the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie regulation of protein localisation to nucleus GOC:TermGenie regulation of protein localization in cell nucleus GOC:TermGenie regulation of protein localization in nucleus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:48Z down regulation of protein localisation to nucleus down regulation of protein localization in cell nucleus down regulation of protein localization in nucleus down regulation of protein localization to nucleus down-regulation of protein localisation to nucleus down-regulation of protein localization in cell nucleus down-regulation of protein localization in nucleus down-regulation of protein localization to nucleus downregulation of protein localisation to nucleus downregulation of protein localization in cell nucleus downregulation of protein localization in nucleus downregulation of protein localization to nucleus negative regulation of protein localisation to nucleus negative regulation of protein localization in cell nucleus negative regulation of protein localization in nucleus inhibition of protein localisation to nucleus inhibition of protein localization in cell nucleus inhibition of protein localization in nucleus inhibition of protein localization to nucleus biological_process GO:1900181 negative regulation of protein localization to nucleus GO:1900181 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie down regulation of protein localisation to nucleus GOC:TermGenie down regulation of protein localization in cell nucleus GOC:TermGenie down regulation of protein localization in nucleus GOC:TermGenie down regulation of protein localization to nucleus GOC:TermGenie down-regulation of protein localisation to nucleus GOC:TermGenie down-regulation of protein localization in cell nucleus GOC:TermGenie down-regulation of protein localization in nucleus GOC:TermGenie down-regulation of protein localization to nucleus GOC:TermGenie downregulation of protein localisation to nucleus GOC:TermGenie downregulation of protein localization in cell nucleus GOC:TermGenie downregulation of protein localization in nucleus GOC:TermGenie downregulation of protein localization to nucleus GOC:TermGenie negative regulation of protein localisation to nucleus GOC:TermGenie negative regulation of protein localization in cell nucleus GOC:TermGenie negative regulation of protein localization in nucleus GOC:TermGenie inhibition of protein localisation to nucleus GOC:TermGenie inhibition of protein localization in cell nucleus GOC:TermGenie inhibition of protein localization in nucleus GOC:TermGenie inhibition of protein localization to nucleus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:52Z activation of protein localization in nucleus positive regulation of protein localisation to nucleus positive regulation of protein localization in cell nucleus positive regulation of protein localization in nucleus up regulation of protein localisation to nucleus up regulation of protein localization in cell nucleus up regulation of protein localization in nucleus up regulation of protein localization to nucleus up-regulation of protein localisation to nucleus up-regulation of protein localization in cell nucleus up-regulation of protein localization in nucleus up-regulation of protein localization to nucleus upregulation of protein localisation to nucleus upregulation of protein localization in cell nucleus upregulation of protein localization in nucleus upregulation of protein localization to nucleus activation of protein localisation to nucleus activation of protein localization in cell nucleus activation of protein localization to nucleus biological_process GO:1900182 positive regulation of protein localization to nucleus GO:1900182 Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie activation of protein localization in nucleus GOC:TermGenie positive regulation of protein localisation to nucleus GOC:TermGenie positive regulation of protein localization in cell nucleus GOC:TermGenie positive regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localisation to nucleus GOC:TermGenie up regulation of protein localization in cell nucleus GOC:TermGenie up regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localization to nucleus GOC:TermGenie up-regulation of protein localisation to nucleus GOC:TermGenie up-regulation of protein localization in cell nucleus GOC:TermGenie up-regulation of protein localization in nucleus GOC:TermGenie up-regulation of protein localization to nucleus GOC:TermGenie upregulation of protein localisation to nucleus GOC:TermGenie upregulation of protein localization in cell nucleus GOC:TermGenie upregulation of protein localization in nucleus GOC:TermGenie upregulation of protein localization to nucleus GOC:TermGenie activation of protein localisation to nucleus GOC:TermGenie activation of protein localization in cell nucleus GOC:TermGenie activation of protein localization to nucleus GOC:TermGenie Binding to nucleoside phosphate. bf 2012-08-17T12:59:58Z molecular_function GO:1901265 nucleoside phosphate binding GO:1901265 Binding to nucleoside phosphate. GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process GO:1901360 The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie Binding to heterocyclic compound. bf 2012-09-14T13:53:50Z molecular_function GO:1901363 heterocyclic compound binding GO:1901363 Binding to heterocyclic compound. GOC:TermGenie The chemical reactions and pathways involving organonitrogen compound. pr 2012-11-04T15:17:52Z organonitrogen compound metabolism biological_process GO:1901564 organonitrogen compound metabolic process GO:1901564 The chemical reactions and pathways involving organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of histone deacetylase activity. rl 2013-01-07T09:14:12Z biological_process GO:1901725 regulation of histone deacetylase activity GO:1901725 Any process that modulates the frequency, rate or extent of histone deacetylase activity. GOC:BHF GOC:TermGenie GOC:rl PMID:20497126 Any process that activates or increases the frequency, rate or extent of histone deacetylase activity. rl 2013-01-07T09:14:21Z up regulation of histone deacetylase activity up-regulation of histone deacetylase activity upregulation of histone deacetylase activity activation of histone deacetylase activity biological_process GO:1901727 positive regulation of histone deacetylase activity GO:1901727 Any process that activates or increases the frequency, rate or extent of histone deacetylase activity. GOC:BHF GOC:TermGenie GOC:rl PMID:20497126 up regulation of histone deacetylase activity GOC:TermGenie up-regulation of histone deacetylase activity GOC:TermGenie upregulation of histone deacetylase activity GOC:TermGenie activation of histone deacetylase activity GOC:TermGenie Any process that modulates the frequency, rate or extent of post-translational protein modification. yaf 2013-02-05T10:02:52Z regulation of PTM regulation of post-translational amino acid modification regulation of post-translational modification regulation of posttranslational amino acid modification regulation of posttranslational modification regulation of posttranslational protein modification biological_process GO:1901873 regulation of post-translational protein modification GO:1901873 Any process that modulates the frequency, rate or extent of post-translational protein modification. GOC:TermGenie GOC:yaf PMID:21209915 regulation of PTM GOC:TermGenie regulation of post-translational amino acid modification GOC:TermGenie regulation of post-translational modification GOC:TermGenie regulation of posttranslational amino acid modification GOC:TermGenie regulation of posttranslational modification GOC:TermGenie regulation of posttranslational protein modification GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of post-translational protein modification. yaf 2013-02-05T10:02:57Z down regulation of PTM down regulation of post-translational amino acid modification down regulation of post-translational modification down regulation of post-translational protein modification down regulation of posttranslational amino acid modification down regulation of posttranslational modification down regulation of posttranslational protein modification down-regulation of PTM down-regulation of post-translational amino acid modification down-regulation of post-translational modification down-regulation of post-translational protein modification down-regulation of posttranslational amino acid modification down-regulation of posttranslational modification down-regulation of posttranslational protein modification downregulation of PTM downregulation of post-translational amino acid modification downregulation of post-translational modification downregulation of post-translational protein modification downregulation of posttranslational amino acid modification downregulation of posttranslational modification downregulation of posttranslational protein modification inhibition of PTM inhibition of post-translational amino acid modification inhibition of post-translational modification inhibition of posttranslational amino acid modification inhibition of posttranslational modification inhibition of posttranslational protein modification negative regulation of PTM negative regulation of post-translational amino acid modification negative regulation of post-translational modification negative regulation of posttranslational amino acid modification negative regulation of posttranslational modification negative regulation of posttranslational protein modification inhibition of post-translational protein modification biological_process GO:1901874 negative regulation of post-translational protein modification GO:1901874 Any process that stops, prevents or reduces the frequency, rate or extent of post-translational protein modification. GOC:TermGenie GOC:yaf PMID:21209915 down regulation of PTM GOC:TermGenie down regulation of post-translational amino acid modification GOC:TermGenie down regulation of post-translational modification GOC:TermGenie down regulation of post-translational protein modification GOC:TermGenie down regulation of posttranslational amino acid modification GOC:TermGenie down regulation of posttranslational modification GOC:TermGenie down regulation of posttranslational protein modification GOC:TermGenie down-regulation of PTM GOC:TermGenie down-regulation of post-translational amino acid modification GOC:TermGenie down-regulation of post-translational modification GOC:TermGenie down-regulation of post-translational protein modification GOC:TermGenie down-regulation of posttranslational amino acid modification GOC:TermGenie down-regulation of posttranslational modification GOC:TermGenie down-regulation of posttranslational protein modification GOC:TermGenie downregulation of PTM GOC:TermGenie downregulation of post-translational amino acid modification GOC:TermGenie downregulation of post-translational modification GOC:TermGenie downregulation of post-translational protein modification GOC:TermGenie downregulation of posttranslational amino acid modification GOC:TermGenie downregulation of posttranslational modification GOC:TermGenie downregulation of posttranslational protein modification GOC:TermGenie inhibition of PTM GOC:TermGenie inhibition of post-translational amino acid modification GOC:TermGenie inhibition of post-translational modification GOC:TermGenie inhibition of posttranslational amino acid modification GOC:TermGenie inhibition of posttranslational modification GOC:TermGenie inhibition of posttranslational protein modification GOC:TermGenie negative regulation of PTM GOC:TermGenie negative regulation of post-translational amino acid modification GOC:TermGenie negative regulation of post-translational modification GOC:TermGenie negative regulation of posttranslational amino acid modification GOC:TermGenie negative regulation of posttranslational modification GOC:TermGenie negative regulation of posttranslational protein modification GOC:TermGenie inhibition of post-translational protein modification GOC:TermGenie Any process that activates or increases the frequency, rate or extent of post-translational protein modification. yaf 2013-02-05T10:03:02Z activation of PTM activation of post-translational amino acid modification activation of post-translational modification activation of posttranslational amino acid modification activation of posttranslational modification activation of posttranslational protein modification positive regulation of PTM positive regulation of post-translational amino acid modification positive regulation of post-translational modification positive regulation of posttranslational amino acid modification positive regulation of posttranslational modification positive regulation of posttranslational protein modification up regulation of PTM up regulation of post-translational amino acid modification up regulation of post-translational modification up regulation of post-translational protein modification up regulation of posttranslational amino acid modification up regulation of posttranslational modification up regulation of posttranslational protein modification up-regulation of PTM up-regulation of post-translational amino acid modification up-regulation of post-translational modification up-regulation of post-translational protein modification up-regulation of posttranslational amino acid modification up-regulation of posttranslational modification up-regulation of posttranslational protein modification upregulation of PTM upregulation of post-translational amino acid modification upregulation of post-translational modification upregulation of post-translational protein modification upregulation of posttranslational amino acid modification upregulation of posttranslational modification upregulation of posttranslational protein modification activation of post-translational protein modification biological_process GO:1901875 positive regulation of post-translational protein modification GO:1901875 Any process that activates or increases the frequency, rate or extent of post-translational protein modification. GOC:TermGenie GOC:yaf PMID:21209915 activation of PTM GOC:TermGenie activation of post-translational amino acid modification GOC:TermGenie activation of post-translational modification GOC:TermGenie activation of posttranslational amino acid modification GOC:TermGenie activation of posttranslational modification GOC:TermGenie activation of posttranslational protein modification GOC:TermGenie positive regulation of PTM GOC:TermGenie positive regulation of post-translational amino acid modification GOC:TermGenie positive regulation of post-translational modification GOC:TermGenie positive regulation of posttranslational amino acid modification GOC:TermGenie positive regulation of posttranslational modification GOC:TermGenie positive regulation of posttranslational protein modification GOC:TermGenie up regulation of PTM GOC:TermGenie up regulation of post-translational amino acid modification GOC:TermGenie up regulation of post-translational modification GOC:TermGenie up regulation of post-translational protein modification GOC:TermGenie up regulation of posttranslational amino acid modification GOC:TermGenie up regulation of posttranslational modification GOC:TermGenie up regulation of posttranslational protein modification GOC:TermGenie up-regulation of PTM GOC:TermGenie up-regulation of post-translational amino acid modification GOC:TermGenie up-regulation of post-translational modification GOC:TermGenie up-regulation of post-translational protein modification GOC:TermGenie up-regulation of posttranslational amino acid modification GOC:TermGenie up-regulation of posttranslational modification GOC:TermGenie up-regulation of posttranslational protein modification GOC:TermGenie upregulation of PTM GOC:TermGenie upregulation of post-translational amino acid modification GOC:TermGenie upregulation of post-translational modification GOC:TermGenie upregulation of post-translational protein modification GOC:TermGenie upregulation of posttranslational amino acid modification GOC:TermGenie upregulation of posttranslational modification GOC:TermGenie upregulation of posttranslational protein modification GOC:TermGenie activation of post-translational protein modification GOC:TermGenie Any process that modulates the frequency, rate or extent of protein acetylation. ss 2013-03-14T00:40:07Z regulation of protein amino acid acetylation biological_process GO:1901983 regulation of protein acetylation GO:1901983 Any process that modulates the frequency, rate or extent of protein acetylation. GOC:TermGenie PMID:22117195 regulation of protein amino acid acetylation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein acetylation. ss 2013-03-14T00:40:19Z positive regulation of protein amino acid acetylation up regulation of protein acetylation up regulation of protein amino acid acetylation up-regulation of protein acetylation up-regulation of protein amino acid acetylation upregulation of protein acetylation upregulation of protein amino acid acetylation activation of protein acetylation activation of protein amino acid acetylation biological_process GO:1901985 positive regulation of protein acetylation GO:1901985 Any process that activates or increases the frequency, rate or extent of protein acetylation. GOC:TermGenie PMID:22117195 positive regulation of protein amino acid acetylation GOC:TermGenie up regulation of protein acetylation GOC:TermGenie up regulation of protein amino acid acetylation GOC:TermGenie up-regulation of protein acetylation GOC:TermGenie up-regulation of protein amino acid acetylation GOC:TermGenie upregulation of protein acetylation GOC:TermGenie upregulation of protein amino acid acetylation GOC:TermGenie activation of protein acetylation GOC:TermGenie activation of protein amino acid acetylation GOC:TermGenie Any process that modulates the frequency, rate or extent of chromatin organization. bf 2013-07-01T13:21:52Z GO:0001672 GO:1903308 regulation of chromatin organisation regulation of establishment or maintenance of chromatin architecture biological_process regulation of chromatin assembly or disassembly regulation of chromatin assembly/disassembly regulation of chromatin modification GO:1902275 regulation of chromatin organization GO:1902275 Any process that modulates the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:bf GOC:vw GO_REF:0000058 PMID:18314879 regulation of chromatin organisation GOC:TermGenie regulation of establishment or maintenance of chromatin architecture GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. dgf 2013-07-29T20:54:14Z down regulation of chromosome condensation down regulation of eukaryotic chromosome condensation down regulation of nuclear chromosome condensation down-regulation of chromosome condensation down-regulation of eukaryotic chromosome condensation down-regulation of nuclear chromosome condensation downregulation of chromosome condensation downregulation of eukaryotic chromosome condensation downregulation of nuclear chromosome condensation negative regulation of eukaryotic chromosome condensation negative regulation of nuclear chromosome condensation inhibition of chromosome condensation inhibition of eukaryotic chromosome condensation inhibition of nuclear chromosome condensation biological_process GO:1902340 negative regulation of chromosome condensation GO:1902340 Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. GOC:TermGenie PMID:23219725 down regulation of chromosome condensation GOC:TermGenie down regulation of eukaryotic chromosome condensation GOC:TermGenie down regulation of nuclear chromosome condensation GOC:TermGenie down-regulation of chromosome condensation GOC:TermGenie down-regulation of eukaryotic chromosome condensation GOC:TermGenie down-regulation of nuclear chromosome condensation GOC:TermGenie downregulation of chromosome condensation GOC:TermGenie downregulation of eukaryotic chromosome condensation GOC:TermGenie downregulation of nuclear chromosome condensation GOC:TermGenie negative regulation of eukaryotic chromosome condensation GOC:TermGenie negative regulation of nuclear chromosome condensation GOC:TermGenie inhibition of chromosome condensation GOC:TermGenie inhibition of eukaryotic chromosome condensation GOC:TermGenie inhibition of nuclear chromosome condensation GOC:TermGenie A protein complex which is capable of acetyltransferase activity. bhm 2013-11-13T16:16:45Z cellular_component GO:1902493 acetyltransferase complex GO:1902493 A protein complex which is capable of acetyltransferase activity. GOC:TermGenie GOC:bhm PMID:8077207 A protein complex which is capable of catalytic activity. https://github.com/geneontology/go-ontology/issues/19980 bhm 2013-11-13T16:18:47Z enzyme complex cellular_component GO:1902494 catalytic complex GO:1902494 A protein complex which is capable of catalytic activity. GOC:TermGenie GOC:bhm PMID:8077207 enzyme complex GOC:bhm GOC:jl A protein complex which is capable of protein serine/threonine kinase activity. bhm 2013-12-06T16:06:12Z cellular_component PDR16 complex dimer PDR16 complex homodimer GO:1902554 An example is IRE1 in S. cerevisiae (UniProt ID P32361) in PMID:18191223 (inferred from direct assay). serine/threonine protein kinase complex GO:1902554 A protein complex which is capable of protein serine/threonine kinase activity. GOC:TermGenie GOC:bhm PMID:18191223 A protein complex which is capable of H4 histone acetyltransferase activity. bhm 2013-12-10T14:43:51Z Hpa3 (homo-)dimer Hpa3 complex cellular_component GO:1902562 An example of this is Hpa2 in yeast [Q06592] in PMID:23775086 [IDA]. H4 histone acetyltransferase complex GO:1902562 A protein complex which is capable of H4 histone acetyltransferase activity. GOC:TermGenie GOC:bhm PMID:23775086 Hpa3 (homo-)dimer PMID:23775086 Hpa3 complex PMID:23775086 A process in which a protein is transported to, or maintained in the pericentric heterochromatin. mah 2014-02-05T16:59:30Z protein localisation in centromeric heterochromatin biological_process GO:1902682 protein localization to pericentric heterochromatin GO:1902682 A process in which a protein is transported to, or maintained in the pericentric heterochromatin. GOC:TermGenie GO_REF:0000087 PMID:20211136 protein localisation in centromeric heterochromatin GOC:TermGenie A protein complex which is capable of protein kinase activity. bhm 2014-04-17T13:52:40Z cellular_component GO:1902911 An example of this is PKM2 in human (P14618) in PMID:24606918 (inferred from direct assay). protein kinase complex GO:1902911 A protein complex which is capable of protein kinase activity. GOC:TermGenie GOC:bhm GO_REF:0000088 PMID:24606918 A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process GO:1903046 A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process GO:1903047 A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A protein complex which is capable of phosphatase activity. bhm 2014-08-13T10:25:32Z cellular_component GO:1903293 An example of this is PTEN in human (P60484) in PMID:24766807 (inferred from direct assay). phosphatase complex GO:1903293 A protein complex which is capable of phosphatase activity. GOC:TermGenie GOC:bhm GO_REF:0000088 PMID:24766807 Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:13Z biological_process GO:1903379 regulation of mitotic chromosome condensation GO:1903379 Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:24Z down regulation of cellular protein localisation down regulation of cellular protein localization down-regulation of cellular protein localisation down-regulation of cellular protein localization downregulation of cellular protein localisation downregulation of cellular protein localization negative regulation of cellular protein localisation negative regulation of cellular protein localization inhibition of cellular protein localisation inhibition of cellular protein localization biological_process GO:1903828 negative regulation of protein localization GO:1903828 Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:33Z positive regulation of cellular protein localisation positive regulation of cellular protein localization up regulation of cellular protein localisation up regulation of cellular protein localization up-regulation of cellular protein localisation up-regulation of cellular protein localization upregulation of cellular protein localisation upregulation of cellular protein localization biological_process GO:1903829 positive regulation of protein localization GO:1903829 Any process that activates or increases the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie A protein complex which is capable of peptidase inhibitor activity. bhm 2015-03-26T10:16:27Z Cathepsin-B - cystatin-A complex cellular_component GO:1904090 An example of this is Cystatin-A in human (UniProt symbol P01040) in PMID:20860624 (inferred from physical interaction). peptidase inhibitor complex GO:1904090 A protein complex which is capable of peptidase inhibitor activity. GOC:TermGenie GOC:bhm GO_REF:0000088 PMID:20860624 A protein complex which is capable of ATPase activity. bhm 2016-02-04T22:13:32Z VPS4 complex cellular_component GO:1904949 An example of this is VPS4 in Saccharomyces cerevisiae (UniProt ID P52917) in PMID:9606181 (inferred from direct assay). ATPase complex GO:1904949 A protein complex which is capable of ATPase activity. GOC:TermGenie GOC:bhm GO_REF:0000088 PMID:9606181 Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:24Z down regulation of establishment of protein localisation down regulation of establishment of protein localization down regulation of protein positioning down regulation of protein recruitment down-regulation of establishment of protein localisation down-regulation of establishment of protein localization down-regulation of protein positioning down-regulation of protein recruitment downregulation of establishment of protein localisation downregulation of establishment of protein localization downregulation of protein positioning downregulation of protein recruitment negative regulation of establishment of protein localisation negative regulation of protein positioning negative regulation of protein recruitment inhibition of establishment of protein localisation inhibition of establishment of protein localization inhibition of protein positioning inhibition of protein recruitment biological_process GO:1904950 negative regulation of establishment of protein localization GO:1904950 Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 down regulation of establishment of protein localisation GOC:TermGenie down regulation of establishment of protein localization GOC:TermGenie down regulation of protein positioning GOC:TermGenie down regulation of protein recruitment GOC:TermGenie down-regulation of establishment of protein localisation GOC:TermGenie down-regulation of establishment of protein localization GOC:TermGenie down-regulation of protein positioning GOC:TermGenie down-regulation of protein recruitment GOC:TermGenie downregulation of establishment of protein localisation GOC:TermGenie downregulation of establishment of protein localization GOC:TermGenie downregulation of protein positioning GOC:TermGenie downregulation of protein recruitment GOC:TermGenie negative regulation of establishment of protein localisation GOC:TermGenie negative regulation of protein positioning GOC:TermGenie negative regulation of protein recruitment GOC:TermGenie inhibition of establishment of protein localisation GOC:TermGenie inhibition of establishment of protein localization GOC:TermGenie inhibition of protein positioning GOC:TermGenie inhibition of protein recruitment GOC:TermGenie Any process that activates or increases the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:32Z positive regulation of establishment of protein localisation positive regulation of protein positioning positive regulation of protein recruitment up regulation of establishment of protein localisation up regulation of establishment of protein localization up regulation of protein positioning up regulation of protein recruitment up-regulation of establishment of protein localisation up-regulation of establishment of protein localization up-regulation of protein positioning up-regulation of protein recruitment upregulation of establishment of protein localisation upregulation of establishment of protein localization upregulation of protein positioning upregulation of protein recruitment activation of establishment of protein localisation activation of establishment of protein localization activation of protein positioning activation of protein recruitment biological_process GO:1904951 positive regulation of establishment of protein localization GO:1904951 Any process that activates or increases the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 positive regulation of establishment of protein localisation GOC:TermGenie positive regulation of protein positioning GOC:TermGenie positive regulation of protein recruitment GOC:TermGenie up regulation of establishment of protein localisation GOC:TermGenie up regulation of establishment of protein localization GOC:TermGenie up regulation of protein positioning GOC:TermGenie up regulation of protein recruitment GOC:TermGenie up-regulation of establishment of protein localisation GOC:TermGenie up-regulation of establishment of protein localization GOC:TermGenie up-regulation of protein positioning GOC:TermGenie up-regulation of protein recruitment GOC:TermGenie upregulation of establishment of protein localisation GOC:TermGenie upregulation of establishment of protein localization GOC:TermGenie upregulation of protein positioning GOC:TermGenie upregulation of protein recruitment GOC:TermGenie activation of establishment of protein localisation GOC:TermGenie activation of establishment of protein localization GOC:TermGenie activation of protein positioning GOC:TermGenie activation of protein recruitment GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. vw 2016-06-03T08:41:08Z biological_process GO:1905213 negative regulation of mitotic chromosome condensation GO:1905213 Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:23219725 Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization. https://github.com/geneontology/go-ontology/issues/22766 pr 2016-06-15T20:14:47Z GO:0045798 GO:1903309 down regulation of chromatin organisation down regulation of chromatin organization down regulation of establishment or maintenance of chromatin architecture down-regulation of chromatin organisation down-regulation of chromatin organization down-regulation of establishment or maintenance of chromatin architecture downregulation of chromatin organisation downregulation of chromatin organization downregulation of establishment or maintenance of chromatin architecture negative regulation of chromatin assembly/disassembly negative regulation of chromatin organisation negative regulation of establishment or maintenance of chromatin architecture inhibition of chromatin assembly or disassembly inhibition of chromatin organisation inhibition of chromatin organization inhibition of establishment or maintenance of chromatin architecture biological_process down regulation of chromatin assembly or disassembly down-regulation of chromatin assembly or disassembly downregulation of chromatin assembly or disassembly negative regulation of chromatin assembly or disassembly negative regulation of chromatin modification GO:1905268 negative regulation of chromatin organization GO:1905268 Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:pr GOC:vw GO_REF:0000058 PMID:654321 down regulation of chromatin organisation GOC:TermGenie down regulation of chromatin organization GOC:TermGenie down regulation of establishment or maintenance of chromatin architecture GOC:TermGenie down-regulation of chromatin organisation GOC:TermGenie down-regulation of chromatin organization GOC:TermGenie down-regulation of establishment or maintenance of chromatin architecture GOC:TermGenie downregulation of chromatin organisation GOC:TermGenie downregulation of chromatin organization GOC:TermGenie downregulation of establishment or maintenance of chromatin architecture GOC:TermGenie negative regulation of chromatin organisation GOC:TermGenie negative regulation of establishment or maintenance of chromatin architecture GOC:TermGenie inhibition of chromatin organisation GOC:TermGenie inhibition of chromatin organization GOC:TermGenie inhibition of establishment or maintenance of chromatin architecture GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromatin organization. https://github.com/geneontology/go-ontology/issues/22766 pr 2016-06-15T20:14:56Z GO:0045799 GO:1903310 positive regulation of chromatin organisation positive regulation of establishment or maintenance of chromatin architecture up regulation of chromatin organisation up regulation of chromatin organization up regulation of establishment or maintenance of chromatin architecture up-regulation of chromatin organisation up-regulation of chromatin organization up-regulation of establishment or maintenance of chromatin architecture upregulation of chromatin assembly or disassembly upregulation of chromatin organisation upregulation of chromatin organization upregulation of establishment or maintenance of chromatin architecture activation of chromatin assembly or disassembly activation of chromatin organisation activation of chromatin organization activation of establishment or maintenance of chromatin architecture stimulation of chromatin assembly or disassembly biological_process positive regulation of chromatin assembly or disassembly positive regulation of chromatin assembly/disassembly positive regulation of chromatin modification up regulation of chromatin assembly or disassembly up-regulation of chromatin assembly or disassembly GO:1905269 positive regulation of chromatin organization GO:1905269 Any process that activates or increases the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:pr GOC:vw GO_REF:0000058 PMID:654321 positive regulation of chromatin organisation GOC:TermGenie positive regulation of establishment or maintenance of chromatin architecture GOC:TermGenie up regulation of chromatin organisation GOC:TermGenie up regulation of chromatin organization GOC:TermGenie up regulation of establishment or maintenance of chromatin architecture GOC:TermGenie up-regulation of chromatin organisation GOC:TermGenie up-regulation of chromatin organization GOC:TermGenie up-regulation of establishment or maintenance of chromatin architecture GOC:TermGenie upregulation of chromatin organisation GOC:TermGenie upregulation of chromatin organization GOC:TermGenie upregulation of establishment or maintenance of chromatin architecture GOC:TermGenie activation of chromatin organisation GOC:TermGenie activation of chromatin organization GOC:TermGenie activation of establishment or maintenance of chromatin architecture GOC:TermGenie A protein complex which is capable of peptidase activity. bhm 2016-08-16T12:49:36Z protease complex tryptase complex cellular_component GO:1905368 An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay). peptidase complex GO:1905368 A protein complex which is capable of peptidase activity. GOC:TermGenie GOC:bhm GO_REF:0000088 PMID:1689240 Any process that modulates the frequency, rate or extent of protein localization to chromatin. pga 2016-11-01T16:33:52Z regulation of protein localisation to chromatin biological_process GO:1905634 regulation of protein localization to chromatin GO:1905634 Any process that modulates the frequency, rate or extent of protein localization to chromatin. GOC:TermGenie GO_REF:0000058 PMID:20889714 regulation of protein localisation to chromatin GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation. bc 2016-11-04T16:43:13Z down regulation of DNA methylation down-regulation of DNA methylation downregulation of DNA methylation inhibition of DNA methylation biological_process GO:1905642 negative regulation of DNA methylation GO:1905642 Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:27336847 down regulation of DNA methylation GOC:TermGenie down-regulation of DNA methylation GOC:TermGenie downregulation of DNA methylation GOC:TermGenie inhibition of DNA methylation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of DNA methylation. bc 2016-11-04T16:43:22Z up regulation of DNA methylation up-regulation of DNA methylation upregulation of DNA methylation activation of DNA methylation biological_process GO:1905643 positive regulation of DNA methylation GO:1905643 Any process that activates or increases the frequency, rate or extent of DNA methylation. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:27336847 up regulation of DNA methylation GOC:TermGenie up-regulation of DNA methylation GOC:TermGenie upregulation of DNA methylation GOC:TermGenie activation of DNA methylation GOC:TermGenie Any process that modulates the frequency, rate or extent of chromosome separation. bhm 2017-01-13T13:55:18Z regulation of rDNA separation biological_process regulation of chromatid release GO:1905818 regulation of chromosome separation GO:1905818 Any process that modulates the frequency, rate or extent of chromosome separation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:21795393 regulation of rDNA separation GOC:TermGenie regulation of chromatid release GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromosome separation. bhm 2017-01-13T13:55:36Z up regulation of chromosome separation up-regulation of chromosome separation upregulation of chromosome separation activation of chromosome separation activation of rDNA separation positive regulation of rDNA separation up regulation of rDNA separation up-regulation of rDNA separation upregulation of rDNA separation biological_process activation of chromatid release positive regulation of chromatid release up regulation of chromatid release up-regulation of chromatid release upregulation of chromatid release GO:1905820 positive regulation of chromosome separation GO:1905820 Any process that activates or increases the frequency, rate or extent of chromosome separation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:21795393 up regulation of chromosome separation GOC:TermGenie up-regulation of chromosome separation GOC:TermGenie upregulation of chromosome separation GOC:TermGenie activation of chromosome separation GOC:TermGenie activation of rDNA separation GOC:TermGenie positive regulation of rDNA separation GOC:TermGenie up regulation of rDNA separation GOC:TermGenie up-regulation of rDNA separation GOC:TermGenie upregulation of rDNA separation GOC:TermGenie activation of chromatid release GOC:TermGenie positive regulation of chromatid release GOC:TermGenie up regulation of chromatid release GOC:TermGenie up-regulation of chromatid release GOC:TermGenie upregulation of chromatid release GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromosome condensation. bhm 2017-01-13T14:13:44Z positive regulation of eukaryotic chromosome condensation positive regulation of nuclear chromosome condensation up regulation of chromosome condensation up regulation of eukaryotic chromosome condensation up regulation of nuclear chromosome condensation up-regulation of chromosome condensation up-regulation of eukaryotic chromosome condensation up-regulation of nuclear chromosome condensation upregulation of chromosome condensation upregulation of eukaryotic chromosome condensation upregulation of nuclear chromosome condensation activation of chromosome condensation activation of eukaryotic chromosome condensation activation of nuclear chromosome condensation biological_process GO:1905821 positive regulation of chromosome condensation GO:1905821 Any process that activates or increases the frequency, rate or extent of chromosome condensation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:17268547 positive regulation of eukaryotic chromosome condensation GOC:TermGenie positive regulation of nuclear chromosome condensation GOC:TermGenie up regulation of chromosome condensation GOC:TermGenie up regulation of eukaryotic chromosome condensation GOC:TermGenie up regulation of nuclear chromosome condensation GOC:TermGenie up-regulation of chromosome condensation GOC:TermGenie up-regulation of eukaryotic chromosome condensation GOC:TermGenie up-regulation of nuclear chromosome condensation GOC:TermGenie upregulation of chromosome condensation GOC:TermGenie upregulation of eukaryotic chromosome condensation GOC:TermGenie upregulation of nuclear chromosome condensation GOC:TermGenie activation of chromosome condensation GOC:TermGenie activation of eukaryotic chromosome condensation GOC:TermGenie activation of nuclear chromosome condensation GOC:TermGenie Binding to a histone methyltransferase enzyme. pr 2013-11-07T11:59:58Z molecular_function GO:1990226 histone methyltransferase binding GO:1990226 Binding to a histone methyltransferase enzyme. GOC:BHF GOC:ame PMID:19486527 A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). bhm 2013-11-12T13:20:12Z cellular_component GO:1990234 transferase complex GO:1990234 A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). GOC:bhm PMID:16540464 A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. bhm 2014-06-04T09:15:24Z DNA damage repair complex WHY1 complex cellular_component GO:1990391 DNA repair complex GO:1990391 A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GOC:bhm PMID:17217467 PMID:20551348 PMID:22749910 PMID:24192350 Transcription factor complex which interacts with E-box regulatory elements in target genes, including Period (Per1, Per2, Per3) and Cryptochrome (Cry1, Cry2), to activate their transcription during the daytime. The CRY-PER complexes inhibit CLOCK-BMAL1-driven transcription in a negative feedback loop to generate circadian rhythms. bhm 2014-10-08T13:10:24Z CLOCK/BMAL complex cellular_component GO:1990513 An example of this is CLOCK in human (O15516) in PMID:23229515 (inferred from physical interaction). CLOCK-BMAL transcription complex GO:1990513 Transcription factor complex which interacts with E-box regulatory elements in target genes, including Period (Per1, Per2, Per3) and Cryptochrome (Cry1, Cry2), to activate their transcription during the daytime. The CRY-PER complexes inhibit CLOCK-BMAL1-driven transcription in a negative feedback loop to generate circadian rhythms. GOC:bhm PMID:23229515 The modification of histone H4 by the removal of an acetyl group from lysine at position 16 of the histone. al 2015-03-02T15:25:56Z biological_process GO:1990678 histone H4-K16 deacetylation GO:1990678 The modification of histone H4 by the removal of an acetyl group from lysine at position 16 of the histone. PMID:17446861 Binding to a section of chromatin that is associated with gene promoter sequences of DNA. sl 2015-08-28T14:48:29Z molecular_function GO:1990841 promoter-specific chromatin binding GO:1990841 Binding to a section of chromatin that is associated with gene promoter sequences of DNA. PMID:19948729 true A macromolecular complex that contains both RNA and protein molecules. pr 2015-11-19T12:26:37Z GO:0030529 GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP protein-RNA complex extracellular ribonucleoprotein complex intracellular ribonucleoprotein complex cellular_component GO:1990904 ribonucleoprotein complex GO:1990904 A macromolecular complex that contains both RNA and protein molecules. GOC:krc GOC:vesicles A protein complex that contains beta-catenin and a member of the T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) family of transcription factors. bf 2015-12-01T16:32:44Z beta-catenin/LEF complex cellular_component beta-catenin/T-cell factor complex beta-catenin/lymphoid enhancer binding factor complex GO:1990907 beta-catenin-TCF complex GO:1990907 A protein complex that contains beta-catenin and a member of the T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) family of transcription factors. GOC:PARL GOC:bf PMID:11751639 PMID:16936075 PMID:20123964 PMID:21075118 PMID:9419974 beta-catenin/LEF complex PMID:8757136 beta-catenin/T-cell factor complex GOC:bf beta-catenin/lymphoid enhancer binding factor complex PMID:8757136 Any process that activates or increases the frequency, rate or extent of DNA-templated DNA replication. mah 2010-09-15T01:37:10Z positive regulation of DNA-dependent DNA replication biological_process GO:2000105 positive regulation of DNA-templated DNA replication GO:2000105 Any process that activates or increases the frequency, rate or extent of DNA-templated DNA replication. GOC:mah Any process that modulates the frequency, rate or extent of ribonucleoprotein complex localization. mah 2010-10-26T10:35:48Z regulation of RNP localization regulation of cellular ribonucleoprotein complex localization regulation of establishment and maintenance of ribonucleoprotein complex localization regulation of ribonucleoprotein complex localisation biological_process GO:2000197 regulation of ribonucleoprotein complex localization GO:2000197 Any process that modulates the frequency, rate or extent of ribonucleoprotein complex localization. GOC:mah regulation of RNP localization GOC:obol regulation of cellular ribonucleoprotein complex localization GOC:obol regulation of establishment and maintenance of ribonucleoprotein complex localization GOC:obol regulation of ribonucleoprotein complex localisation GOC:mah Any process that modulates the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:02Z biological_process GO:2000241 regulation of reproductive process GO:2000241 Any process that modulates the frequency, rate or extent of reproductive process. GOC:mah Any process that activates or increases the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:08Z biological_process GO:2000243 positive regulation of reproductive process GO:2000243 Any process that activates or increases the frequency, rate or extent of reproductive process. GOC:mah Any process that modulates the frequency, rate or extent of peptidyl-lysine acetylation. yaf 2011-06-16T09:51:26Z biological_process GO:2000756 regulation of peptidyl-lysine acetylation GO:2000756 Any process that modulates the frequency, rate or extent of peptidyl-lysine acetylation. GOC:obol Any process that activates or increases the frequency, rate or extent of peptidyl-lysine acetylation. yaf 2011-06-16T09:51:35Z biological_process GO:2000758 positive regulation of peptidyl-lysine acetylation GO:2000758 Any process that activates or increases the frequency, rate or extent of peptidyl-lysine acetylation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:20Z negative regulation of chromosome organisation biological_process negative regulation of chromosome organization and biogenesis negative regulation of maintenance of genome integrity negative regulation of nuclear genome maintenance GO:2001251 negative regulation of chromosome organization GO:2001251 Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. GOC:obol negative regulation of chromosome organisation GOC:obol negative regulation of chromosome organization and biogenesis GOC:obol negative regulation of maintenance of genome integrity GOC:obol negative regulation of nuclear genome maintenance GOC:obol Any process that activates or increases the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:26Z positive regulation of chromosome organisation biological_process positive regulation of chromosome organization and biogenesis positive regulation of maintenance of genome integrity positive regulation of nuclear genome maintenance GO:2001252 positive regulation of chromosome organization GO:2001252 Any process that activates or increases the frequency, rate or extent of chromosome organization. GOC:obol positive regulation of chromosome organisation GOC:obol positive regulation of chromosome organization and biogenesis GOC:obol positive regulation of maintenance of genome integrity GOC:obol positive regulation of nuclear genome maintenance GOC:obol information content entity information content entity organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality PATO:0000001 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform PATO:0000402 branched PATO:0000402 A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. PATO:0001199 linear PATO:0001199 A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. ISBN:0881923214 A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. 2009-10-06T04:37:14Z PATO:0002124 laminar PATO:0002124 A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 http://www.jbiomedsem.com/content/4/1/43 system Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure UBERON:0000061 anatomical structure UBERON:0000061 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBbt:00005099 NLX:147821 funiculus nerve fiber bundle neural fiber bundle UBERON:0000122 neuron projection bundle UBERON:0000122 A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 nerve fiber bundle FBbt:00005099 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 UBERON:0000465 material anatomical entity UBERON:0000465 Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity UBERON:0000466 immaterial anatomical entity UBERON:0000466 Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 immaterial physical anatomical entity FMA:67112 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 UBERON:0001062 anatomical entity UBERON:0001062 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure UBERON:0010000 multicellular anatomical structure UBERON:0010000 An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313 phenotype ChromatinRegulator CovalentHistoneModifierProtein MethylationModifier AcetylationModifier PhosphorylationModifier SumoylationModifier UbiquitinylationModifier CitrullinationModifier ADP-ribosylationModifier HistoneAcetyltransferase HistoneDeacetylase Domain SAMD1-like winged helix (WH) JmjC C2HC MYST-type C2H2-type ARID Post-SET PHD-type 3 Helicase C-terminal Bromo PHD-type 2 divergent MYST-type HAT C5HC2 Chromo 1 FYR C-terminal PHD-type 1 N-acetyltransferase SET PWWP H15 JmjN C2HC pre-PHD-type CXXC-type Chromo 2 FYR N-terminal PHD-type 4 Helicase ATP-binding HistoneUbiquitinLigase HistoneDeubiquitinase C2H2-type 8 PAS 1 C2H2-type 1 BAH C2H2-type 2 C6-type YDG Deacetylase sirtuin-type Protein kinase 2 DHHC RING-type 3 C2H2-type 11 PHD-type 5 Chromo C2H2-type 7 WW Bromo 1 TAZ-type 1 RING-type PAS bHLH Tudor-knot PWWP 2 C2H2-type 10 PHD-type 6 C2H2-type 6 MBD F-box UBP-type MYND-type PHD-type 7 Pre-SET RRM DOT1 C2H2-type 3 PAC KIX C2H2-type 4 AWS CW-type CXC atypical SAM-dependent MTase PRMT-type KRAB-related C2H2-type 5 C2H2-type 13 PHD-type 8 MRG TAZ-type 2 FCS-type CCHHC-type SAM-dependent MTase PRMT-type 2 PAS 2 PHD-type Bromo 2 RING-type 2 Protein kinase 1 C2H2-type 14 RING-type 1 ZZ-type C2HC pre-PHD-type 2 CBP/p300-type HAT SH3 degenerate C2H2-type 9 SGF29 C-terminal C2H2-type 12 Tudor 1 SAM-dependent MTase PRMT-type 1 Tudor 2 PWWP 1 C2HC pre-PHD-type 1 SWIRM Ubiquitin-like HistoneMethyltransferase HistoneDemethylase HistoneKinase HistonePhosphatase CFP1 CGBP PCCX1 PHF18 CXXC1 CHD3 CHD4 CBP CREBBP P300 EP300 GCN5 GCN5L2 KAT2A ALL1 CXXC7 HRX HTRX MLL MLL1 TRX1 KMT2A CENP-35 KIAA0662 PHF2 JARID1A RBBP2 RBP2 KDM5A KMT1A SUV39H SUV39H1 BA2R CCG1 CCGS TAF2A TAF1 TAF2A TAF2H TAFII30 TAF10 KIAA1090 MMSET TRX5 WHSC1 NSD2 MOZ MYST3 RUNXBP2 ZNF220 KAT6A AF10 MLLT10 DXS1272E JARID1C SMCX XE169 KDM5C EED PCAF KAT2B WBSC10 WBSCR10 WBSCR9 WSTF BAZ1B CDY1A CDY1 CDY2 CDY2A KIAA0026 MRGX MORF4L2 JHDM3A JMJD2 JMJD2A KIAA0677 KDM4A KIAA0215 PHF16 JADE3 JARID1B PLU1 RBBP2H1 KDM5B SMAP SMAP2 BRD8 BAT8 C6orf30 G9A KMT1C NG36 EHMT2 MRG15 MORF4L1 MSL3L1 MSL3 BIG3 WDR5 GASC1 JHDM3C JMJD2C KIAA0780 KDM4C KIAA1111 ZNF422 PHF8 KIAA0239 PHF15 JADE2 KIAA0383 MORF MOZ2 MYST4 KAT6B ICBP90 NP95 RNF106 UHRF1 PHF20L1 ING4 C20orf104 GLEA2 HCA58 NZF TZP PHF20 WDR5B ING3 MBTD1 WHSC1L1 NSD3 KIAA1420 KMT2H ASH1L EUHMTASE1 GLP KIAA1876 KMT1D EHMT1 KIAA1807 PHF17 JADE1 JHDM1D KDM7 KIAA1718 KDM7A ING5 CCDC101 SGF29 TAF1L C5orf7 JHDM2B JMJD1B KIAA1082 KDM3B KIAA0288 HDAC4 RPD3L1 HDAC1 HDAC2 JMJ JARID2 UTX KDM6A KDM6C UTY HY HYA JARID1D KIAA0234 SMCY KDM5D HDAC3 HDAC7 HDAC7B HDRP KIAA0744 MITR HDAC9 KIAA0901 HDAC6 KIAA0600 HDAC5 SIR2L SIR2L2 SIRT2 CXXC8 FBL11 FBL7 FBXL11 JHDM1A KIAA1004 KDM2A AOF2 KDM1 KIAA0601 LSD1 KDM1A JHDM3B JMJD2B KIAA0876 KDM4B JMJD3 KIAA0346 KDM6B KIAA0585 PSR PTDSR JMJD6 SIR2L4 SIRT4 SIR2L3 SIRT3 SIR2L1 SIRT1 SIR2L7 SIRT7 SIR2L6 SIRT6 HDAC7A HDAC7 JHDM3D JMJD2D KDM4D HR JHDM2A JMJD1 JMJD1A KIAA0742 TSGA KDM3A HDACL1 HDAC8 C14orf169 MAPJD NO66 RIOX1 JMJD5 KDM8 HDAC11 HDAC10 CXXC2 FBL10 FBXL10 JHDM1B NDY1 PCCX2 KDM2B MDIG MINA MINA53 NO52 RIOX2 JHDM2C KIAA1380 TRIP8 JMJD1C AOF1 C6orf193 LSD2 KDM1B KDM4DL KDM4E SETMAR EVI1 MDS1 PRDM3 MECOM EYA1 KIAA0388 EZH1 KMT6 EZH2 HMT1 HRMT1L1 PRMT2 HMT2 HRMT1L2 IR1B4 PRMT1 KMT8 RIZ PRDM2 ALR MLL2 MLL4 KMT2D AIB1 BHLHE42 RAC3 TRAM1 NCOA3 KAT1 HAT1 BHLHE74 SRC1 NCOA1 GTF3C4 BHLHE8 KIAA0334 CLOCK KIAA0339 KMT2F SET1 SET1A SETD1A HRX2 KIAA0304 MLL2 MLL4 TRX2 WBP7 KMT2B ESET KIAA0067 KMT1E SETDB1 HRMT1L5 IBP72 JBP1 SKB1 PRMT5 PRMT4 CARM1 HTATIP TIP60 KAT5 PFM4 PRDM7 HBO1 HBOa MYST2 KAT7 KIAA1076 KMT2G SET1B SETD1B HIF1 HYPB KIAA1732 KMT3A SET2 SETD2 SUV420H1 KMT5B KIAA1933 PRMT7 HRMT1L6 PRMT6 HRMT1L3 HRMT1L4 PRMT8 KMT3C SMYD2 PFM6 PRDM9 CSRP2BP KAT14 HALR KIAA1506 MLL3 KMT2C KIAA1675 MEL1 PFM13 PRDM16 ARA267 KMT3B NSD1 ZMYND1 ZNFN3A1 SMYD3 KMT1B SUV39H2 NAT11 PATT1 NAA40 KIAA1717 KMT7 SET7 SET9 SETD7 C13orf4 CLLD8 KMT1F SETDB2 MOF MYST1 KAT8 C14orf154 SETD3 KIAA1814 KMT4 DOT1L SUV420H2 KMT5C SMYD1 PRSET7 SET07 SET8 SETD8 KMT5A HistoneTarget H2ATarget H2BTarget H3Target H4Target H3K27ME3 H4K8 H3K27ME2 H2A H3K122 H3K36ME H3K9ME H3R2 H3K23 H4K20 H3K4ME H3R8 H3R3 H3K9ME2 H3K9 H3K4ME3 H4K16 H3K9ME3 H3K4ME2 H3K27 H3K36ME3 H4K12 H3K14 H3 H3K36ME2 H4R3 H3K79 H2B H3K36 H2AR3 H4K5 H3K56 H3K18 H3K4 H3R17 H4 H2AX H4K20ME H2AK5 ChromatinRemodelerComplex 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 SWI/SNFComplex 1 1 1 1 1 1 cBAFComplex 1 1 1 GBAFComplex 1 1 1 1 PBAFComplex ATP-DependentChromatinRemodelerComplex SMARCC1 SMARCC2 SMARCA4 SMARCA2 SMARCB1 SMARCE1 SMARCD1 SMARCD2 SMARCD3 ACTB ACTL6A ACTL6B BCL7A BCL7B BCL7C SYT SSXT ChromatinRegulatorProtein ARID1A ARID1B DPF2 DPF3 BCL11A BCL11B ARID2 PBRM1 BRD7 PHF10 BRD9 BICRA BICRAL ISWIComplex 1 1 ACF 1 1 1 RSF 1 1 1 CERF 1 1 1 1 CHRAC 1 1 1 1 NURF 1 1 NoRC 1 1 WICH 1 1 1 1 1 1 1 1 b-WICH SNF2H ACF1 RSF1 SNF2L CECR2 CHRAC15 CHRAC17 BPTF RBAP46 RBAP48 TIP5 WSTF DEK CSB NMI SF3B1 MYBBP1A RHII CHD1 CHD2 CHD5 CHD6 CHD7 CHD8 CHD9 MTA1 MTA2 MTA3 GATAD2A GATAD2B MBD2 MBD3 1 1 1 1 1 1 1 1 1 CHDComplex 1 1 1 1 1 1 1 1 1 1 1 1 1 NuRD 1 1 1 1 1 NuRD-like INO80 RUVBL1 RUVBL2 MCRS1 AMIDA YY1 IES6 IES2 UCH37 NFRKB INO80E p400 TRRAP EPC1 EPC2 YL-1 GAS41 DMAP1 FLJ11730 MRG15 MRGX MRGBP SRCAP ARP6 ZnF-HIT1 1 1 1 INO80Complex 1 1 1 1 1 1 1 1 1 1 1 1 INO80 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Tip60/p400 1 1 1 1 1 1 1 1 1 SRCAP GNATProtein MYSTProtein p300/CBPProtein HistoneLysineMethyltransferase SET1Protein SET2Protein EZHProtein SYMDProtein SUV39Protein PRDMProtein owl:Nothing example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument Researcher Austin Meier Researcher Austin Meier researcher Shawn Zheng Kai Tan researcher Shawn Zheng Kai Tan researcher, metadata, diseases, University of Maryland Lynn Schriml researcher, metadata, diseases, University of Maryland Lynn Schriml data scientist Anne Thessen data scientist Anne Thessen researcher Pier Luigi Buttigieg researcher Pier Luigi Buttigieg bioinformatics researcher Christopher J. Mungall bioinformatics researcher Christopher J. Mungall researcher David Osumi-Sutherland researcher David Osumi-Sutherland researcher Lauren E. Chan researcher Lauren E. Chan researcher Marie-Angélique Laporte researcher Marie-Angélique Laporte researcher James P. Balhoff researcher James P. Balhoff researcher Lindsay G Cowell researcher Lindsay G Cowell researcher Anna Maria Masci researcher Anna Maria Masci American chemist Charles Tapley Hoyt American chemist Charles Tapley Hoyt 2023-06-11 2023-08-18 has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external has_part has_part has part has part occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in https://wiki.geneontology.org/Occurs_in cjm 2012-03-14T10:35:44Z GOREL:0000040 external results_in results_in This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change. results in GOREL:0001019 external results_in_division_of results_in_division_of use occurs_in results in division of GOREL:0002003 external results_in_distribution_of results_in_distribution_of results in distribution of GOREL:0002004 external results_in_fission_of results_in_fission_of results in fission of GOREL:0012006 external results_in_maintenance_of results_in_maintenance_of results in maintenance of data item data item data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. out of scope This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms abbreviation A synonym type for describing ambiguous synonyms ambiguous synonym A synonym type for describing dubious synonyms dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants UK spelling synonym A synonym type for common misspellings misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name legal name p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. Gene Ontology The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology gene_ontology 1.2 2023-06-11 2023-08-18 https://github.com/oborel/obo-relations/ true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).