BDgene

Core Gene from Gene Prioritization Pathways from PBA (Pathway-based Analysis) Enriched Pathways for Core Genes Enriched Pathways for Cross-disorder Genes

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Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	IFNG
Approved Name	interferon, gamma
Location	12q14
Position	chr12:68154768-68159747, -1
External Links	HGNC: 5438 Entrez Gene: 3458 Ensembl: ENSG00000111537 UCSC: uc001stw.1
No. of Studies	2 (Positive: 2; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Yoon, H. K.,2012	SNP: rs2430561	Our results suggest that the IFNG+874A/T polymorphism may have important effects related to susceptibility to BD and that the T allele may be associated with an increased risk of developing BD.	Positive	Comment on Study
Clerici, M.,2009	Other variant: IFNG_874T/A	Our data reported a different genotype and allele distribution of -308 TNF-Î± and +874 IFN-Î³ in the bipolar II group that showed a higher percentage of subjects characterized by a lower production of both cytokines.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 69)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0009615	response to virus	biological process	IDA[16280321]	5
GO:0005125	cytokine activity	molecular function	IBA	13

GO terms by database search (count: 67)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0006915	apoptotic process	biological process	IGI[7828849]	39
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	ISS	62
GO:0032224	positive regulation of synaptic transmission, cholinergic	biological process	IEA	2
GO:2000309	positive regulation of tumor necrosis factor (ligand) superfamily member 11 production	biological process	IDA[16220542]	1
GO:0007166	cell surface receptor signaling pathway	biological process	TAS[10477596]	23
GO:0042493	response to drug	biological process	IEA	57
GO:0050796	regulation of insulin secretion	biological process	IDA[8383325]	24
GO:0048304	positive regulation of isotype switching to IgG isotypes	biological process	IEA	1
GO:0060334	regulation of interferon-gamma-mediated signaling pathway	biological process	TAS	2
GO:0002026	regulation of the force of heart contraction	biological process	IEA	5
GO:0045080	positive regulation of chemokine biosynthetic process	biological process	IEA	3
GO:0044130	negative regulation of growth of symbiont in host	biological process	IEA	5
GO:0098908	regulation of neuronal action potential	biological process	IEA	1
GO:0060552	positive regulation of fructose 1,6-bisphosphate metabolic process	biological process	IDA[9282826]	1
GO:0060550	positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity	biological process	IDA[9282826]	1
GO:0003340	negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis	biological process	IEA	1
GO:0071222	cellular response to lipopolysaccharide	biological process	IEA	12
GO:0045084	positive regulation of interleukin-12 biosynthetic process	biological process	IEA	2
GO:0002250	adaptive immune response	biological process	IBA	5
GO:0060559	positive regulation of calcidiol 1-monooxygenase activity	biological process	IDA[9282826]	3
GO:0071351	cellular response to interleukin-18	biological process	IEA	1
GO:0005133	interferon-gamma receptor binding	molecular function	IEA	1
GO:0042742	defense response to bacterium	biological process	IEA	4
GO:0000060	protein import into nucleus, translocation	biological process	IDA[15604419]	4
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IEA	91
GO:0045666	positive regulation of neuron differentiation	biological process	IEA	8
GO:0050718	positive regulation of interleukin-1 beta secretion	biological process	IEA	3
GO:0005615	extracellular space	cellular component	IBA	85
GO:0051044	positive regulation of membrane protein ectodomain proteolysis	biological process	IDA[18373975]	5
GO:0060557	positive regulation of vitamin D biosynthetic process	biological process	IDA[9282826]	2
GO:0042511	positive regulation of tyrosine phosphorylation of Stat1 protein	biological process	IDA[15604419]	1
GO:0031642	negative regulation of myelination	biological process	IEA	3
GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	biological process	IDA[16280321]; NAS[21268089]	1
GO:0019221	cytokine-mediated signaling pathway	biological process	TAS	23
GO:0001781	neutrophil apoptotic process	biological process	IEA	3
GO:2000345	regulation of hepatocyte proliferation	biological process	IEA	1
GO:0010634	positive regulation of epithelial cell migration	biological process	IDA[11698262]	5
GO:0072308	negative regulation of metanephric nephron tubule epithelial cell differentiation	biological process	IEA	1
GO:0002302	CD8-positive, alpha-beta T cell differentiation involved in immune response	biological process	IEA	1
GO:0032735	positive regulation of interleukin-12 production	biological process	IDA[7605994]	5
GO:0009897	external side of plasma membrane	cellular component	IEA	21
GO:0060333	interferon-gamma-mediated signaling pathway	biological process	TAS	10
GO:0042102	positive regulation of T cell proliferation	biological process	IEA	6
GO:0008284	positive regulation of cell proliferation	biological process	ISS	44
GO:0032760	positive regulation of tumor necrosis factor production	biological process	IEA	5
GO:0045348	positive regulation of MHC class II biosynthetic process	biological process	IEA	5
GO:0034393	positive regulation of smooth muscle cell apoptotic process	biological process	IDA[16942485]	2
GO:0045429	positive regulation of nitric oxide biosynthetic process	biological process	IDA[8383325]	13
GO:0045672	positive regulation of osteoclast differentiation	biological process	IDA[16220542]	5
GO:0005576	extracellular region	cellular component	IDA[20041150]; TAS	97
GO:0042832	defense response to protozoan	biological process	IEA	3
GO:0006928	movement of cell or subcellular component	biological process	TAS[10477596]	7
GO:0051607	defense response to virus	biological process	IEA	6
GO:0030968	endoplasmic reticulum unfolded protein response	biological process	IEA	10
GO:0050954	sensory perception of mechanical stimulus	biological process	IEA	1
GO:0002053	positive regulation of mesenchymal cell proliferation	biological process	IEA	3
GO:0045410	positive regulation of interleukin-6 biosynthetic process	biological process	IEA	2
GO:0006959	humoral immune response	biological process	IBA	5
GO:0030857	negative regulation of epithelial cell differentiation	biological process	ISS	1
GO:0019882	antigen processing and presentation	biological process	IEA	2
GO:0032747	positive regulation of interleukin-23 production	biological process	IDA[20027291]	2
GO:0051712	positive regulation of killing of cells of other organism	biological process	IDA[7544003]	1
GO:0032700	negative regulation of interleukin-17 production	biological process	IDA[18501882]	2
GO:0007050	cell cycle arrest	biological process	IDA[16942485]	10
GO:0048662	negative regulation of smooth muscle cell proliferation	biological process	IDA[16942485]	7
GO:0097191	extrinsic apoptotic signaling pathway	biological process	IDA[16942485]	5
GO:0030593	neutrophil chemotaxis	biological process	IEA	8

Gene related KEGG pathways (count: 10)

KEGG pathways by PBA (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04350	TGF-beta signaling pathway	10
hsa04140	Regulation of autophagy	3

KEGG pathways by database search (count: 8)

ID	Name	No. of Genes in BDgene
hsa05322	Systemic lupus erythematosus	4
hsa05330	Allograft rejection	6
hsa05332	Graft-versus-host disease	7
hsa04060	Cytokine-cytokine receptor interaction	17
hsa04650	Natural killer cell mediated cytotoxicity	13
hsa04940	Type I diabetes mellitus	10
hsa04660	T cell receptor signaling pathway	13
hsa04630	Jak-STAT signaling pathway	14

Gene related BioCarta pathways (count: 13)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 13)

ID	Name	No. of Genes in BDgene
cytokinePathway	Cytokine Network	4
th1th2Pathway	Th1/Th2 Differentiation	1
il18Pathway	IL 18 Signaling Pathway	2
41bbPathway	The 4-1BB-dependent immune response	1
inflamPathway	Cytokines and Inflammatory Response	4
no2il12Pathway	NO2-dependent IL 12 Pathway in NK cells	1
dcPathway	Dendritic cells in regulating TH1 and TH2 Development	3
ifngPathway	IFN gamma signaling pathway	2
IL12Pathway	IL12 and Stat4 Dependent Signaling Pathway in Th1 Development	2
tob1Pathway	Role of Tob in T-cell activation	1
tidPathway	Chaperones modulate interferon Signaling Pathway	3
granulocytesPathway	Adhesion and Diapedesis of Granulocytes	2
nktPathway	Selective expression of chemokine receptors during T-cell polarization	1

Gene related interactors from protein-protein interactions data in HPRD (count: 3)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
IFNG	IFNGR1	NO	in vitro;in vivo	12165521 , 10986460 , 11250200
IFNG	PDIA3	NO	in vivo	8974399
IFNG	IFNGR2	NO	in vivo	7673114

Related other genetic factors

Gene related SNPs (count: 1)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2430561	chr12:68158742 - 68158742(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)

LD-proxies (count: 0)

Gene related CNVs (count: 0)

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
IFNG_874T/A	point mutation		1 (1/0/0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 12	chr12:0-133275309	3 (0/3/0)
12q	chr12:38200000-133851895	1 (1/0/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with SZ from candidate gene intersection analysis (count: 1)

Reference	ID in SZGene	Result Category
20821074	977	Positive

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 0)

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
20479761	Gene set analysis suggested up-regulation of a variety of pro- and anti-inflammatory cytokines, including interleukin 1alpha (IL-1alpha), IL-2, IL-3, IL-5, IL-8, IL-9, IL-10, IL-12A, IL-13, IL-15, IL-18, interferon gamma (IFNgamma), and lymphotoxin alpha (TNF superfamily member 1).	Pos	IFNG

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Region: chr12:68154768..68159747 View in gBrowse