Gene Page: IRF4

Summary ?
GeneID3662
SymbolIRF4
SynonymsLSIRF|MUM1|NF-EM5|SHEP8
Descriptioninterferon regulatory factor 4
ReferenceMIM:601900|HGNC:HGNC:6119|Ensembl:ENSG00000137265|HPRD:03543|Vega:OTTHUMG00000016294
Gene typeprotein-coding
Map location6p25.3
Pascal p-value0.921
Fetal beta-0.194
DMG1 (# studies)
eGeneMeta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
GSMA_IGenome scan meta-analysisPsr: 0.0159 
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg062237676393616IRF48.83E-7-0.3020.007DMG:Wockner_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
LILRB10.720.63
FGD20.720.70
AC055839.10.710.69
DEF60.700.71
PRAM10.680.71
P2RX70.670.70
COBL0.670.68
CSF3R0.670.71
WDFY40.670.68
TPPP0.670.64
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RPSA-0.40-0.53
RPL18-0.40-0.58
TUBB2B-0.39-0.43
RPL5-0.39-0.50
RPL24-0.39-0.56
RPL35-0.39-0.54
PPP1R14B-0.39-0.56
RPS6-0.39-0.55
RPS3P3-0.39-0.54
RPS9-0.38-0.53

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityNAS8657101 |12374808 
GO:0003702RNA polymerase II transcription factor activityTAS8921401 
GO:0008134transcription factor bindingNAS12374808 
GO:0016563transcription activator activityIDA12374808 
GO:0016563transcription activator activityISS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0043011myeloid dendritic cell differentiationIEAdendrite (GO term level: 10)-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006355regulation of transcription, DNA-dependentNAS8657101 
GO:0042110T cell activationNAS12374808 
GO:0045368positive regulation of interleukin-13 biosynthetic processIDA12374808 
GO:0045368positive regulation of interleukin-13 biosynthetic processISS-
GO:0045622regulation of T-helper cell differentiationNAS12374808 
GO:0045941positive regulation of transcriptionIDA12374808 
GO:0045941positive regulation of transcriptionISS-
GO:0045086positive regulation of interleukin-2 biosynthetic processIDA12374808 
GO:0045086positive regulation of interleukin-2 biosynthetic processISS-
GO:0045082positive regulation of interleukin-10 biosynthetic processIDA12374808 
GO:0045082positive regulation of interleukin-10 biosynthetic processISS-
GO:0045404positive regulation of interleukin-4 biosynthetic processIDA12374808 
GO:0045404positive regulation of interleukin-4 biosynthetic processISS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIC12374808 
GO:0005634nucleusNAS8657101 
GO:0005737cytoplasmIDA18029348 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID IL4 2PATHWAY 6543All SZGR 2.0 genes in this pathway
PID NFAT TFPATHWAY 4739All SZGR 2.0 genes in this pathway
REACTOME INTERFERON GAMMA SIGNALING 6348All SZGR 2.0 genes in this pathway
REACTOME INTERFERON ALPHA BETA SIGNALING 6450All SZGR 2.0 genes in this pathway
REACTOME INTERFERON SIGNALING 159116All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933616All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM 270204All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP 579346All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D UP 175108All SZGR 2.0 genes in this pathway
BILBAN B CLL LPL UP 6339All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION MONOCYTE DN 5438All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA DN 284156All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN 12073All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
KLEIN TARGETS OF BCR ABL1 FUSION 4534All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 15 139All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN 712443All SZGR 2.0 genes in this pathway
FUNG IL2 SIGNALING 2 128All SZGR 2.0 genes in this pathway
FUNG IL2 TARGETS WITH STAT5 BINDING SITES T1 97All SZGR 2.0 genes in this pathway
TSAI RESPONSE TO IONIZING RADIATION 149101All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP 283177All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 2 3023All SZGR 2.0 genes in this pathway
MORI SMALL PRE BII LYMPHOCYTE UP 8657All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE UP 7851All SZGR 2.0 genes in this pathway
BROCKE APOPTOSIS REVERSED BY IL6 14498All SZGR 2.0 genes in this pathway
KLEIN PRIMARY EFFUSION LYMPHOMA UP 5129All SZGR 2.0 genes in this pathway
SASAKI ADULT T CELL LEUKEMIA 176122All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN 366238All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION UP 11484All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293193All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING UP 10176All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION 405264All SZGR 2.0 genes in this pathway
SU THYMUS 2012All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR UP 10573All SZGR 2.0 genes in this pathway
SAFFORD T LYMPHOCYTE ANERGY 8754All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253147All SZGR 2.0 genes in this pathway
GAVIN FOXP3 TARGETS CLUSTER T4 9469All SZGR 2.0 genes in this pathway
ZHENG BOUND BY FOXP3 491310All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
ZHENG FOXP3 TARGETS IN THYMUS UP 196137All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN 281179All SZGR 2.0 genes in this pathway
WORSCHECH TUMOR REJECTION UP 5632All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN 546362All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323240All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE 346192All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP 338225All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP 418282All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 DN 245150All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12 317177All SZGR 2.0 genes in this pathway
SHAFFER IRF4 MULTIPLE MYELOMA PROGRAM 3625All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN PLASMA CELL VS MATURE B LYMPHOCYTE 6751All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN ACTIVATED B LYMPHOCYTE 8166All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN ACTIVATED DENDRITIC CELL 6549All SZGR 2.0 genes in this pathway
ZHAN EARLY DIFFERENTIATION GENES UP 76All SZGR 2.0 genes in this pathway
ONO AML1 TARGETS DN 4125All SZGR 2.0 genes in this pathway
ONO FOXP3 TARGETS DN 4223All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS DN 11674All SZGR 2.0 genes in this pathway
KASLER HDAC7 TARGETS 1 UP 194133All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D 658397All SZGR 2.0 genes in this pathway
BOSCO ALLERGEN INDUCED TH2 ASSOCIATED MODULE 15186All SZGR 2.0 genes in this pathway
BOSCO TH1 CYTOTOXIC MODULE 11462All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-125/3515925991A,m8hsa-miR-125bbrainUCCCUGAGACCCUAACUUGUGA
hsa-miR-125abrainUCCCUGAGACCCUUUAACCUGUG
miR-1284364431A,m8hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
miR-274374441A,m8hsa-miR-27abrainUUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrainUUCACAGUGGCUAAGUUCUGC
miR-30-5p4614681A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA