Ontology for Disease Genetic Investigation
type: Ontology
creator: Yu Lin
version info: 1.0
comment: Author contact: Yu Lin (linikujp@gmail.com)
comment: It is the ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .
comment: The modeling documents including two papers: 1. Ontology of Genetic Susceptibility Factors to Diabetes Mellitus (OGSF-DM) http://www.academia.edu/213769/Ontology_of_Genetic_Susceptibility_Factors_to_Diabetes_Mellitus_OGSF-DM_ 2. Ontology driven modeling for the knowledge of genetic susceptibility to disease. http://www.ncbi.nlm.nih.gov/pubmed/19628970
imports: swrla.owl
imports: query.owl
imports: swrlx.owl
imports: temporal.owl
imports: http://www.ifomis.org/bfo/1.1
imports: swrl
imports: swrlb

isGeneProductOf
type: ObjectProperty
comment: maybe sequence product?
range: Gene
domain: Gene Product

GenomicSequence
type: DatatypeProperty
range: Datatype
  one of: DNA
  one of: RNA

ABI 3100 Avant Genetic Analyzer
type: Class
subclass of: Hardware
comment: ABI 3100 Avant Genetic Analyzer (Applied Biosystems)

Antigen
type: Class
subclass of: Protein
comment: Substances that are recognized by the immune system and induce an immune reaction.(MeSH)

Benjamini-Hochberg method
type: Class
subclass of: Method of Statistical Study
comment: P values were corrected for multiple tests using the Benjamini-Hochberg method.

Biological Process
type: Class
subclass of: Process
comment: GO: biological process

Biological Role
type: Class
subclass of: Role
disjoint with: Non Biological Role
comment: The role which is taken by biological things(such as moleculars, cells) when they involed in a biological process, such as auto immune process, etc. its different with function.examples: a protein plays antigen role in an autoimmune process.

Biological Techniques
type: Class
subclass of: Investigative Techniques
comment: the technology used for dealing with biological things,such as molecular, virus, animals, gene,in molecular biology, immunology fields. you can say the wet experiment technologies.the objects of biological techniques are biological things, and the result from biological techniques is biological. Thus, the measurement of body, glucose tolerance test are not biological techniques.

Carrier Frequncy
type: Class
subclass of: Frequency
comment: frequncy of the observed genetic factors in different group of the studied population. REF:Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease or: allele frequncy?

Causation
type: Class
subclass of: Related
comment: For example, a mutation in X gene cause the Y disease, then, they hold a causation relationship.

Classified Group
type: Class
subclass of: Human Collective
subclass of: Restriction
  on property: isPartOf
  all values from: Study Population
comment: is the divided group of the study population;

Continuant
type: Class
subclass of: Entity
disjoint with: Occurrent
comment: BFO: SPAN: Continuant
comment: Comments: This universal has also been called ‘endurant’.
comment: Df: 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. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra,the disposition of blood to coagulate, the lawn and atmosphere in front of the White House.

Copy Number Polymorphism
type: Class
subclass of: Polymorphisms
comment: SO:0001019

Dependent Continuant
type: Class
subclass of: Continuant
comment: Comments: This universal is also sometimes referred to by the name ‘property’, ‘trope’ or ‘mode’.
comment: Df: The continuant entities that inhere in or are born by other entities. Examples: the mass of a cloud, the color of a tomato, the smell of mozzarella, the liquidity of blood, the disposition of fish to decay, the role of being a doctor, the function of the heart to pump blood. (BFO)

Disease Gene Study in Paper
type: Class
subclass of: Disease Gene Research
subclass of: Restriction
  on property: hasStudyPopulation
  some values from: Study Population
subclass of: Restriction
  on property: hasPubMedID
  some values from: PubMedID
comment: original paper which study the disease and gene relationship.

Entrez MapViewer
type: Class
subclass of: Software
comment: Entrez MapViewer (build 33).

Fishers exact test
type: Class
subclass of: Method of Statistical Study
comment: Fisher's exact test

Gene
type: Class
subclass of: Genetic Object
subclass of: Restriction
  on property: hasObservedRelationship
  some values from: Observed Relationship
subclass of: Restriction
  on property: hasGeneSequence
  all values from: DNA Sequence of Gene
subclass of: Restriction
  on property: isRelatedGeneOf
  some values from: Genetic Variant
subclass of: Restriction
  on property: hasHGNCsymbol
  all values from: HGNC Symbol
subclass of: Restriction
  on property: hasGeneDatabaseID
  some values from: Gene Database ID
subclass of: Restriction
  on property: hasNonHgncSymbol
  some values from: Non HGNC Symbol
subclass of: Restriction
  on property: hasGeneSequence
  some values from: DNA Sequence of Gene
subclass of: Restriction
  on property: hasAlleleofgenes
  some values from: Allele of Genes
comment: the instance is gene name which is written in the article.

Gene Product
type: Class
subclass of: Biological Object
subclass of: Restriction
  on property: isGeneProductOf
  some values from: Gene
comment: generally Product means functional product, maybe sequence product?

Genome
type: Class
subclass of: Genomic Collective
comment: It is a term used to describe the total genetic information(DNA content) in human cells.

Genomic Sequence
type: Class
subclass of: Genetic Object
comment: the phisical sequence of a given gene

Hardy-Weinberg Equilibrium
type: Class
subclass of: Method
comment: Hardy-Weinberg equilibrium (HWE)

IBD Allele
type: Class
subclass of: Allele Shared by Sibs
comment: Allele which is shared among sibs is identical by desent(idb),which means, this allele comes from the same person of parents.

IBS Allele
type: Class
subclass of: Allele Shared by Sibs
comment: Allele which is shared among sibs is identical by state, which means, the allele may comes from both of their parents.

Independent Continuant
type: Class
subclass of: Continuant
comment: Independent Continuant
comment: Comments: This universal has also been called ‘substantial entity’.
comment: Df: The continuant entities that are the bearers of qualities and realizables; entities in which other entities inhere and which themselves cannot inhere in anything. Examples: an organism, a heart, a symphony orchestra, a chair, the bottom right portion of a human torso, a leg, a person, a symphony orchestra, the lawn and atmosphere in front of the White House.

Investigative Techniques
type: Class
subclass of: Non Biological Object
comment: Definition: Investigative techniques used in pre-clinical and clinical research, epidemiology, chemistry, immunology, genetics, etc. They do not include techniques specifically applied to DIAGNOSIS; THERAPEUTICS; anesthesia and analgesia; SURGICAL PROCEDURES, OPERATIVE; and DENTISTRY. (MeSH)

LINE1
type: Class
subclass of: Long Interspersed Nucleotide Elements
comment: L1 family

Lamda o
type: Class
subclass of: Relative Risk Index
comment: lamda for offspring

Lamda s
type: Class
subclass of: Relative Risk Index
comment: lamda for sibs

Linked Locus
type: Class
subclass of: Genomic Region
subclass of: Restriction
  on property: hasGeneticMarker
  some values from: Genetic Marker
comment: is the locus defined by the linkage study based on LOD scores of the genetic markers

Long Interspersed Nucleotide Elements
type: Class
subclass of: Repeat DNA Sequence
comment: LINES

Long Terminal Repeats
type: Class
subclass of: Repeat DNA Sequence
comment: LTRs

MLS
type: Class
subclass of: LOD Score
comment: Maximum-likelihood LOD score(MLS). MLS may be interpreted, as the ratio of the probability that a given obeservational outcome would occur if the trait and marker loci were linked to the probability that it would occur if they were unlinked. (Gustavo Maroni, 2001, Molecular and Genetic Analysis of Human Traits, p46)

Microsatellite DNA
type: Class
subclass of: Repeat DNA Sequence
comment: STR or microsatellite DNA has repeating units of 2 to 5 bases. Such as simple repetitive elements, (CA)n, (AAT)n, (GATA)n, also called simple sequence DNA, existing in thousands of loci in the human genome.
comment: also STR, Short tandem repeats

Minisatellite DNA
type: Class
subclass of: Repeat DNA Sequence
comment: Definition: Minisatellite DNA are sequences in which repeating units occur in blocks of up to 50kb. Repeating units are between 10 and 200 bases in length.
comment: also VNTR, Variable number tandem repeats

Molecular Function
type: Class
subclass of: Biological Function
comment: Same with GO: Molecular function

National Project
type: Class
subclass of: Disease Gene Research
subclass of: Restriction
  on property: hasStudyPopulation
  some values from: Study Population
subclass of: Restriction
  on property: hasGeographicalSite
  some values from: Geographical Site
comment: Instances such as FUSION study, etc.

Non Biological Role
type: Class
subclass of: Role
comment: any role when it is not biological role; such as a SNP's role as a maker in associate study. Or, this role is not comes from the biological things function, but, is assigned by human being.

Non Biological Techniques
type: Class
subclass of: Investigative Techniques
comment: the technology used for dealing with non-biological things, such as: numbers, data,etc.

Observed Relationship
type: Class
subclass of: Statistical Observation
subclass of: Restriction
  on property: isRelationshipWith
  some values from: Class
    union of: Human Disease
    union of: Measurement
    union of: Phenotype
    union of: Population Characteristic
subclass of: Restriction
  on property: hasSupportingEvidence
  all values from: Supporting Evidence
subclass of: Restriction
  on property: isObservedIn
  some values from: Disease Gene Study in Paper
subclass of: Restriction
  on property: hasPopulation
  all values from: Study Population
subclass of: Class
  union of: Not Related
  union of: Related
subclass of: Restriction
  on property: isObservedRelationshipOf
  some values from: Class
    union of: Genetic Object
    union of: Genomic Collective
    union of: Statistical Interaction
comment: Obeserved_Relationship is the relationship between a genetic things with disease or related traits, which is observed by linkage or association study in genetic studies field. for example: related, susceptibility, association, and so on.

Population Group
type: Class
subclass of: Study Population
comment: is the population studied in case-control, when the sample is the single individual, but not family,nor trios.nor pairs

Proband
type: Class
subclass of: Human
comment: Proband is the first affected family member who seeks medical attention for a genetic disorder.(wikipedia)

Process Entitiy
type: Class
subclass of: Occurrent
comment: Df: an occurrent entity that exists in time by occurring or happening, has temporal parts, and always depends on some SNAP entity or entities. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird, the process of cell division.

Quantitative Data Entity
type: Class
subclass of: GenericallyDependentContinuant
comment: all the subclass holds the data, for example, instance of age is 40, instance of Odds_Ratio is 1.47

Relative Risk Index
type: Class
subclass of: Quantitative Data Entity
comment: Definition: Relative risk index (lamda),express the degree to which a relative of a patient is more likely than a non relative to suffer a given syndrome.(Gustavo Maroni, 2001, Molecular and Genetic Analysis of Human Traits, p38 )

Restriction Fragment Length Polymorphisms
type: Class
subclass of: Polymorphisms
comment: RFLPs

Role
type: Class
subclass of: Dependent Continuant
subclass of: Class
  union of: Biological Role
  union of: Non Biological Role
comment: in chinese 角色

SNP
type: Class
subclass of: Polymorphisms
subclass of: Restriction
  on property: hasAlleleComponent
  some values from: SNP Allele Component
comment: SO:0000694
comment: Single Nucleotide Polymorphism

STR Polymorphism
type: Class
subclass of: Repeat Sequnce Polymorphism
comment: microsatellite polymorphism

Satellite DNA
type: Class
subclass of: Repeat DNA Sequence
comment: highly repeated DNA

Sequence Localization Relationship
type: Class
subclass of: GenericallyDependentContinuant
comment: the localization relationship between genomic sequences. for example:a genetic marker is contained in a gene. or a haplotype is contained in a gene. (get idea from gdb)

Short Interspersed Nucleotide Elements
type: Class
subclass of: Repeat DNA Sequence
comment: SINES

Statistical Interaction
type: Class
subclass of: Statistical Observation
subclass of: Restriction
  on property: hasObservedRelationship
  some values from: Observed Relationship
subclass of: Restriction
  on property: hasInteractFactor
  min cardinality: 2

Supporting Evidence
type: Class
subclass of: Quantitative Data Entity
subclass of: Restriction
  on property: hasClassifiedGroup
  some values from: Classified Group
subclass of: Restriction
  on property: isSupportingEvidenceOf
  all values from: Observed Relationship
subclass of: Restriction
  on property: hasP
  some values from: P Value
comment: he supporting evidence has classified group when it states the classified group with the OR(for example), sometimes the paper didn't declare the classified group with the supporting evidence, then we don't not need to list out the classified group.

Type 1 Diabetes A
type: Class
subclass of: Type 1 Diabetes
comment: According to the classification of WHO, Type 1 Diabetes A is autoimmune Diabetes type.

VNTR Polymorphism
type: Class
subclass of: Repeat Sequnce Polymorphism
comment: VNTR is Minisatellite DNA

X 2 test
type: Class
subclass of: Method of Statistical Study
comment: X{chi}2 test

dHPLC
type: Class
subclass of: Biological Techniques
comment: denaturing high-performance liquid chromatography [dHPLC]

htSNPs
type: Class
subclass of: SNPs
comment: haplotype-tag single nucleotide polymorphisms

A genome-wide search for human non-insulin-dependent type 2 diabetes genes reveals a major susceptibility locus on chromosome 2
type: NamedIndividual
type: Disease Gene Study in Paper
comment: A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2
has pub med ID: PMID_8640221
has study population: Sib Pairs Collective 1

An Autosomal Genomic Scan for Loci Linked to Type II Diabetes Mellitus and Body-Mass Index in Pima Indians
type: NamedIndividual
type: Disease Gene Study in Paper
comment: An Autosomal Genomic Scan for Loci Linked to Type II Diabetes Mellitus and Body-Mass Index in Pima Indians
has abstract URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi
has full URL: http://www.pubmedcentral.nih.gov/picrender.fcgi
has pub med ID: PMID_9758619
has study population: Pima Indian

Association of genetic variations near P2 promoter of the hepatocyte nuclear factor 4alpha gene and insulin secretion index in Thais
type: NamedIndividual
type: Disease Gene Study in Paper
comment: Association of genetic variations near P2 promoter of the hepatocyte nuclear factor-4alpha gene and insulin secretion index in Thais.
has pub med ID: PMID_17805472
has study population: Thais 1

Case Group 1
type: NamedIndividual
type: Classified Group
has population size: 275
has population characteristic: Case Group
is part of: an ashkenazi jewish population
has population characteristic: type 2 diabetic patients

Common variants of the novel type 2 diabetes genes CDKAL1 and HHEX IDE are associated with decreased pancreatic beta-cell function
type: NamedIndividual
type: Disease Gene Study in Paper
comment: Common variants of the novel type 2 diabetes genes, CDKAL1 and HHEX/IDE, are associated with decreased pancreatic {beta}-cell function
has pub med ID: PMID_17804762
has study population: healthy subjects of European ancestry

Contained Inside 2
type: NamedIndividual
type: Contained Inside
comment: by Ensembl map view
has localization subject: glycerol-3-phosphate dehydrogenase 1-like

Control Group 1
type: NamedIndividual
type: Classified Group
has population size: 342
has population characteristic: Contorl Group
has population characteristic: Healthy control subjects
is part of: an ashkenazi jewish population

Control Group 2
type: NamedIndividual
type: Classified Group
has population size: 138
has population characteristic: Healthy 1
is part of: a Caucasian population

Controls 1
type: NamedIndividual
type: Classified Group
has population size: 2890
has population characteristic: Healthy 1
is part of: general Dutch population

Corrected P 0.0252
type: NamedIndividual
type: Corrected P
has pvalue: 0.0252

Cytogenetic Band 3p24.2-3p22
type: NamedIndividual
type: Cytogenetic Band
comment: information from GDB
is part cytogenetic band of: Choromosome 3
is part cytogenetic band of: Choromosome 3q

D11S4464
type: NamedIndividual
type: Microsatellite Marker
comment: the strongest from the article
has chromosome locus: Choromosome 11
has marker database ID: GDB_683022
has marker database ID: GDB_683508
has observed relationship: Linkage 10
has observed relationship: Linkage 9
has localization relation: Start Region
has marker database ID: UniSTS 8547

FUSION study
type: NamedIndividual
type: National Project
comment: Finland-United States Investigation of NIDDM Genetics study
has geographical site: Europe
has geographical site: Finland
has geographical site: North America
has geographical site: U.S.

Family Collective 1
type: NamedIndividual
type: Family Collective
has population size: 52
has population characteristic: Family collecitve
has population characteristic: more than one member affected with insulin-dependent diabetes mellitus

Frequency 1
type: NamedIndividual
type: Frequency
has frequency: 0.29
is frequency in: Case Group 1
is allele frequency of: Rare Allele of SNP 1

Frequency 2
type: NamedIndividual
type: Frequency
has frequency: 0.217
is frequency in: Control Group 1
is allele frequency of: Rare Allele of SNP 1

Frequency 3
type: NamedIndividual
type: Frequency
has frequency: 0.806
is allele frequency of: Allele of INS VNTR Class 1
is frequency in: LADA group

Frequency 4
type: NamedIndividual
type: Frequency
has frequency: 0.813
is allele frequency of: Allele of INS VNTR Class 1
is frequency in: Type 1 Diabetes Group 1

Frequency 5
type: NamedIndividual
type: Frequency
has frequency: 0.7
is allele frequency of: Allele of INS VNTR Class 1
is frequency in: Control Group 2

Frequency 6
type: NamedIndividual
type: Frequency
has frequency: 0.636
is frequency in: LADA group

Frequency 7
type: NamedIndividual
type: Frequency
has frequency: 0.37
is frequency in: Type 1 Diabetes Group 1

Frequency 8
type: NamedIndividual
type: Frequency
has frequency: 0.534
is frequency in: Type 1 Diabetes Group 1

Frequency 9
type: NamedIndividual
type: Frequency
has frequency: 1
is allele frequency of: Allele of INS VNTR 1S
is frequency in: LADA group

Genomewide Search for Type 2 Diabetes Susceptibility Genes in Four American Populations
type: NamedIndividual
type: Disease Gene Study in Paper
comment: Genomewide Search for Type 2 Diabetes Susceptibility Genes in Four American Populations
has abstract URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi
has full URL: http://www.pubmedcentral.nih.gov/picrender.fcgi
has study population: Four American Populations
has pub med ID: PMID_10793009

Healthy control subjects
type: NamedIndividual
type: Healthy
comment: control (n = 342) subjects

Japanese American 128
type: NamedIndividual
type: Classified Group
has population size: 128
is part population of: Four American Populations
has population characteristic: Japanese American

LADA group
type: NamedIndividual
type: Classified Group
has population size: 275
has population characteristic: Patients with LADA
is part of: a Caucasian population

LOD Score 1.87
type: NamedIndividual
type: LOD Score
has LOD: 0
is supporting evidence of: Linkage 9

LOD Score 2.39
type: NamedIndividual
type: LOD Score
has LOD: 2.39
is supporting evidence of: Linkage 8
has classified group: a African American 229

LOD Score 2.63
type: NamedIndividual
type: LOD Score
has LOD: 2.63
is supporting evidence of: Linkage 10

LOD Score 2.80
type: NamedIndividual
type: LOD Score
has LOD: 2.80
is supporting evidence of: Linkage 4
has classified group: Mexican American 591

LOD Score 2.81
type: NamedIndividual
type: LOD Score
has LOD: 0
is supporting evidence of: Linkage 5
has classified group: a White Group

LOD Score 2.88
type: NamedIndividual
type: LOD Score
has LOD: 2.88
is supporting evidence of: Linkage 2

LOD Score 2.99
type: NamedIndividual
type: LOD Score
has LOD: 2.99
is supporting evidence of: Linkage 6
has classified group: a White Group

LOD Score 3.75
type: NamedIndividual
type: LOD Score
has LOD: 3.75
is supporting evidence of: Linkage 3

LOD Score 3.91
type: NamedIndividual
type: LOD Score
has LOD: 3.91
is supporting evidence of: Linkage 7
has classified group: Mexican American 591

LPIN2 is associated with type 2 diabetes glucose metabolism and body composition
type: NamedIndividual
type: Disease Gene Study in Paper
comment: LPIN2 is associated with type 2 diabetes, glucose metabolism and body composition
has pub med ID: PMID_17804763
has study population: general Dutch population

Linkage of Type 2 Diabetes Mellitus and of Age at Onset to a Genetic Location on Chromosome 10q in Mexican Americans
type: NamedIndividual
type: Disease Gene Study in Paper
comment: Linkage of Type 2 Diabetes Mellitus and of Age at Onset to a Genetic Location on Chromosome 10q in Mexican Americans
has abstract URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi
has full URL: http://www.pubmedcentral.nih.gov/picrender.fcgi
has pub med ID: PMID_10090898
has study population: Population Group 46

MLS 3.20
type: NamedIndividual
type: MLS
has LOD: 0
is supporting evidence of: Linkage 1
has p: P Value 0.0001

MODY 1
type: NamedIndividual
type: MODY1
comment: MODY is a clinically and genetically heterogeneous form of nonketotic diabetes that presents before age 25 years, usually in nonobese, asymptomatic, hyperglycemic individuals.
comment: maturity-onset diabetes of the young (MODY)-1

Max Copy Number of Repeat Unit 159
type: NamedIndividual
type: Max Copy Number of Repeat Unit
has copy number: 159

Max Copy Number of Repeat Unit 37
type: NamedIndividual
type: Max Copy Number of Repeat Unit
has copy number: 37

Max Copy Number of Repeat Unit 43
type: NamedIndividual
type: Max Copy Number of Repeat Unit
has copy number: 43

Max Copy Number of Repeat Unit 44
type: NamedIndividual
type: Max Copy Number of Repeat Unit
has copy number: 44

Max Copy Number of Repeat Unit 46
type: NamedIndividual
type: Max Copy Number of Repeat Unit
has copy number: 46

Mexican American 591
type: NamedIndividual
type: Classified Group
has population size: 591
is part population of: Four American Populations
has population characteristic: Mexican American

Min Copy Number of Repeat Unit 138
type: NamedIndividual
type: Min Copy Number of Repeat Unit
has copy number: 138

Min Copy Number of Repeat Unit 21
type: NamedIndividual
type: Min Copy Number of Repeat Unit
has copy number: 21

Min Copy Number of Repeat Unit 38
type: NamedIndividual
type: Min Copy Number of Repeat Unit
has copy number: 38

Min Copy Number of Repeat Unit 42
type: NamedIndividual
type: Min Copy Number of Repeat Unit
has copy number: 42

Odds Ratio 2.01
type: NamedIndividual
type: Odds Ratio
has OR: 2.01
has classified group: Controls 1
has p: P Value 0.03
has classified group: T2D cases
is supporting evidence of: associated with 6

PMID_10090898
type: NamedIndividual
type: PubMedID
has publication date: 1999 Mar
is pub med ID of: Linkage of Type 2 Diabetes Mellitus and of Age at Onset to a Genetic Location on Chromosome 10q in Mexican Americans
is ID component of: PubMed

PMID_15047632
type: NamedIndividual
type: PubMedID
has publication date: 2004 Apr
is pub med ID of: A Common Polymorphism in the Upstream Promoter Region of the Hepatocyte Nuclear Factor-4 alpha Gene on Chromosome 20q Is Associated With Type 2 Diabetes and Appears to Contribute to the Evidence for Linkage in an Ashkenazi Jewish Population
is ID component of: PubMed

PMID_15230641
type: NamedIndividual
type: PubMedID
has publication date: 2004
is ID component of: PubMed
is pub med ID of: Variable number of tandem repeats of the insulin gene determines susceptibility to latent autoimmune diabetes in adults

PMID_17804762
type: NamedIndividual
type: PubMedID
has publication date: 2007 Sep 5; [Epub ahead of print]
is pub med ID of: Common variants of the novel type 2 diabetes genes CDKAL1 and HHEX IDE are associated with decreased pancreatic beta-cell function
is ID component of: PubMed

PMID_17804763
type: NamedIndividual
type: PubMedID
has publication date: 2007 Oct 24; [Epub ahead of print]
is pub med ID of: LPIN2 is associated with type 2 diabetes glucose metabolism and body composition
is ID component of: PubMed

PMID_17805472
type: NamedIndividual
type: PubMedID
has publication date: 2007 Sep
is pub med ID of: Association of genetic variations near P2 promoter of the hepatocyte nuclear factor 4alpha gene and insulin secretion index in Thais
is ID component of: PubMed

PMID_8640221
type: NamedIndividual
type: PubMedID
has publication date: 1996 Jun
is pub med ID of: A genome-wide search for human non-insulin-dependent type 2 diabetes genes reveals a major susceptibility locus on chromosome 2
is ID component of: PubMed

P Value 0.0000985
type: NamedIndividual
type: P Value
has pvalue: 0.0000985
is supporting evidence of: associated with 5

P Value 0.0001
type: NamedIndividual
type: P Value
has pvalue: 0.0001
is supporting evidence of: Linkage 1

P Value 0.0002
type: NamedIndividual
type: P Value
has pvalue: 0.0002
is supporting evidence of: associated with 2

P Value 0.0002
type: NamedIndividual
type: P Value
has pvalue: 0.0002
is supporting evidence of: associated with 3

P Value 0.009
type: NamedIndividual
type: P Value
has pvalue: 0.009
is supporting evidence of: associated with 4

P Value 0.02
type: NamedIndividual
type: P Value
has pvalue: 0.02
has classified group: Controls 1
has classified group: T2D cases
is supporting evidence of: associated with 7

P Value 0.03
type: NamedIndividual
type: P Value
has pvalue: 0.03

Population Group 46
type: NamedIndividual
type: Population Group
has population size: 579
has population characteristic: Mexican American
has population characteristic: Pedigree 47
has geographical site: U.S.

Risk Ratio 1
type: NamedIndividual
type: Risk Ratio
has RR: 2.282
has classified group: LADA group
has classified group: Type 1 Diabetes Group 1
is supporting evidence of: relative risk 1

Risk Ratio 2
type: NamedIndividual
type: Risk Ratio
has RR: 1.497
has classified group: Control Group 2
has classified group: Type 1 Diabetes Group 1
is supporting evidence of: relative risk 2

Sib Pairs Collective 1
type: NamedIndividual
type: Sibships Collective
has population size: 424
has population characteristic: Mexican American
has population characteristic: Sibships
has geographical site: Starr County
has geographical site: Texas
has geographical site: U.S.

T2D cases
type: NamedIndividual
type: Classified Group
has population size: 616
is part of: general Dutch population
has population characteristic: type 2 diabetic patients

Type 1 Diabetes Group 1
type: NamedIndividual
type: Classified Group
has population size: 88
has population characteristic: Type 1 Diabetes Patients
is part of: a Caucasian population

Uncorrected P 0.0028
type: NamedIndividual
type: Uncorrected P
has pvalue: 0.0028

a 3 intronic SNP rs3818247
type: NamedIndividual
type: htSNP
comment: a 3' intronic SNP
has allele component: DNA Level Allele G
has allele component: DNA Level Allele T
has variant database ID: HGVBase SNP002310533
has observed relationship: associated with 1
has variant database ID: dbSNP rs3818247
has genomic site: flanking 3 intronic
has related gene: hepatocyte nuclear factor-4 alpha

a African American 229
type: NamedIndividual
type: Classified Group
has population size: 0
has population characteristic: Black in U.S.
is part population of: Four American Populations

a White Group
type: NamedIndividual
type: Classified Group
has population size: 835
is part population of: Four American Populations
has population characteristic: White in U.S.

about 1 cM telomeric nearby
type: NamedIndividual
type: Close
comment: ~ 1 cM telomeric to the marker D10S587
has localization subject: about 1 cM telomeric to D10S587

glycerol-3-phosphate dehydrogenase 1-like
type: NamedIndividual
type: Gene
comment: many loci shows in UniSTS, but GPD1L is contained by D3S2432 in Ensembl's map view
is related gene of: D3S2432
has gene database ID: Ensembl ENSG00000152642
has gene database ID: EntrezGene_23171
has HGN csymbol: GPD1L
has gene database ID: GeneCard GC03P032123
has gene database ID: HGNC_28956

healthy subjects of European ancestry
type: NamedIndividual
type: Population Group
has population size: 1276
has population characteristic: Healthy 1
has geographical site: U.K.

hepatocyte nuclear factor-4 alpha
type: NamedIndividual
type: Gene
comment: hepatocyte nuclear factor-4 alpha (HNF4 alpha),
has gene database ID: Ensembl ENSG00000101076
has gene database ID: EntrezGene 3172
has gene database ID: GeneCard GC20P042463
has gene database ID: HGNC 5024
has HGN csymbol: HNF4A
has non hgnc symbol: HNF4 alpha

high BMI
type: NamedIndividual
type: BMI
comment: Body Mass Index

latent autoimmune diabetes in adults
type: NamedIndividual
type: Type 1 Diabetes A
comment: LADA

normal glucose tolerant controls
type: NamedIndividual
type: Classified Group
has population size: 0
has population characteristic: Contorl Group
is part population of: Thais 1

odds ratio OR 1.49
type: NamedIndividual
type: Odds Ratio
has pvalue: 0.0028
has CI95: 1.15-1.90
has OR: 1.49
comment: odds ratio [OR] 1.49
has classified group: Case Group 1
is result of: Case control study 1
has classified group: Control Group 1
has p: Corrected P 0.0252
has p: Uncorrected P 0.0028
is supporting evidence of: associated with 1

prediabetes subjects
type: NamedIndividual
type: Classified Group
has population size: 228
is part population of: Thais 1
has population characteristic: prediabetes

unrelated type 2 diabetes group
type: NamedIndividual
type: Classified Group
has population size: 219
is part population of: Thais 1
has population characteristic: unrelated type 2 diabetes

deleted
comment: Entrez MapViewer build 33