Gene Page: GTF2H4

Summary ?
GeneID2968
SymbolGTF2H4
SynonymsP52|TFB2|TFIIH
Descriptiongeneral transcription factor IIH subunit 4
ReferenceMIM:601760|HGNC:HGNC:4658|Ensembl:ENSG00000213780|HPRD:03456|Vega:OTTHUMG00000031043
Gene typeprotein-coding
Map location6p21.3
Pascal p-value1.428E-13
Sherlock p-value0.002
Fetal beta0.08
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_IGenome scan meta-analysisPsr: 0.033 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg11571001630881808GTF2H41.08E-10-0.0444.65E-7DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs3845734chr2171125572GTF2H429680.15trans
rs6936144chr6156089368GTF2H429680.09trans
rs946457chr6159785798GTF2H429680.09trans
rs2939687chr856313877GTF2H429680.13trans
rs2514332chr899110122GTF2H429680.02trans
rs11038039chr1144530644GTF2H429680trans
rs11038047chr1144543848GTF2H429680.01trans
rs11229308chr1158001840GTF2H429680.01trans
rs17134794chr1176008848GTF2H429689.757E-4trans
rs17730920chr1334267676GTF2H429680.18trans
rs17061055chr1340835399GTF2H429680.02trans
rs1426798chrX17152333GTF2H429680.17trans

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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityTAS9118947 
GO:0003702RNA polymerase II transcription factor activityIEA-
GO:0005515protein bindingIPI17466626 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000718nucleotide-excision repair, DNA damage removalEXP10583946 
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006367transcription initiation from RNA polymerase II promoterEXP8946909 
GO:0006368RNA elongation from RNA polymerase II promoterEXP9405375 
GO:0006350transcriptionIEA-
GO:0006281DNA repairTAS9118947 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005654nucleoplasmEXP1939271 |2449431 |8946909 
|9512541 |9582279 
|9790902 |10214908 
|11313499 |12393749 
|12646563 
GO:0005675holo TFIIH complexTAS9118947 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG BASAL TRANSCRIPTION FACTORS 3624All SZGR 2.0 genes in this pathway
KEGG NUCLEOTIDE EXCISION REPAIR 4425All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION TERMINATION 2212All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION 8964All SZGR 2.0 genes in this pathway
REACTOME RNA POL II TRANSCRIPTION 10554All SZGR 2.0 genes in this pathway
REACTOME MRNA CAPPING 3011All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION COUPLED NER TC NER 4524All SZGR 2.0 genes in this pathway
REACTOME RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 4121All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING 16186All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION 210127All SZGR 2.0 genes in this pathway
REACTOME NUCLEOTIDE EXCISION REPAIR 5127All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX 4519All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX 3013All SZGR 2.0 genes in this pathway
REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 12280All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 11259All SZGR 2.0 genes in this pathway
REACTOME RNA POL II PRE TRANSCRIPTION EVENTS 6132All SZGR 2.0 genes in this pathway
REACTOME GLOBAL GENOMIC NER GG NER 3520All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF INCISION COMPLEX IN GG NER 2311All SZGR 2.0 genes in this pathway
REACTOME HIV INFECTION 207122All SZGR 2.0 genes in this pathway
REACTOME HIV LIFE CYCLE 12569All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF THE HIV1 EARLY ELONGATION COMPLEX 3411All SZGR 2.0 genes in this pathway
REACTOME LATE PHASE OF HIV LIFE CYCLE 10461All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION INITIATION 2514All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 48HR UP 12895All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 96HR UP 11784All SZGR 2.0 genes in this pathway
WAKASUGI HAVE ZNF143 BINDING SITES 5833All SZGR 2.0 genes in this pathway
HUMMERICH SKIN CANCER PROGRESSION DN 10064All 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
BENPORATH ES CORE NINE CORRELATED 10068All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
GENTILE UV LOW DOSE UP 2719All SZGR 2.0 genes in this pathway
ZHANG RESPONSE TO CANTHARIDIN DN 6946All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
LABBE TGFB1 TARGETS DN 10864All SZGR 2.0 genes in this pathway
MOOTHA PGC 420269All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS FIBROBLAST UP 8460All SZGR 2.0 genes in this pathway
YAGI AML WITH INV 16 TRANSLOCATION 422277All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 718401All SZGR 2.0 genes in this pathway
MIKKELSEN NPC ICP WITH H3K4ME3 445257All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242146All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP 10772All SZGR 2.0 genes in this pathway