Gene Page: GTF2H4
Summary ?
GeneID | 2968 |
Symbol | GTF2H4 |
Synonyms | P52|TFB2|TFIIH |
Description | general transcription factor IIH subunit 4 |
Reference | MIM:601760|HGNC:HGNC:4658|Ensembl:ENSG00000213780|HPRD:03456|Vega:OTTHUMG00000031043 |
Gene type | protein-coding |
Map location | 6p21.3 |
Pascal p-value | 1.428E-13 |
Sherlock p-value | 0.002 |
Fetal beta | 0.08 |
DMG | 1 (# studies) |
eGene | Myers' cis & trans |
Gene in Data Sources
Gene set name | Method of gene set | Description | Info |
---|---|---|---|
CV:PGCnp | Genome-wide Association Study | GWAS | |
DMG:Jaffe_2016 | Genome-wide DNA methylation analysis | This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. | 1 |
GSMA_I | Genome scan meta-analysis | Psr: 0.033 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
---|---|---|---|---|---|---|---|
cg11571001 | 6 | 30881808 | GTF2H4 | 1.08E-10 | -0.044 | 4.65E-7 | DMG:Jaffe_2016 |
eQTL annotation
SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
---|---|---|---|---|---|---|---|---|
rs3845734 | chr2 | 171125572 | GTF2H4 | 2968 | 0.15 | trans | ||
rs6936144 | chr6 | 156089368 | GTF2H4 | 2968 | 0.09 | trans | ||
rs946457 | chr6 | 159785798 | GTF2H4 | 2968 | 0.09 | trans | ||
rs2939687 | chr8 | 56313877 | GTF2H4 | 2968 | 0.13 | trans | ||
rs2514332 | chr8 | 99110122 | GTF2H4 | 2968 | 0.02 | trans | ||
rs11038039 | chr11 | 44530644 | GTF2H4 | 2968 | 0 | trans | ||
rs11038047 | chr11 | 44543848 | GTF2H4 | 2968 | 0.01 | trans | ||
rs11229308 | chr11 | 58001840 | GTF2H4 | 2968 | 0.01 | trans | ||
rs17134794 | chr11 | 76008848 | GTF2H4 | 2968 | 9.757E-4 | trans | ||
rs17730920 | chr13 | 34267676 | GTF2H4 | 2968 | 0.18 | trans | ||
rs17061055 | chr13 | 40835399 | GTF2H4 | 2968 | 0.02 | trans | ||
rs1426798 | chrX | 17152333 | GTF2H4 | 2968 | 0.17 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)

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 function | GO term | Evidence | Neuro keywords | PubMed ID |
---|---|---|---|---|
GO:0003700 | transcription factor activity | TAS | 9118947 | |
GO:0003702 | RNA polymerase II transcription factor activity | IEA | - | |
GO:0005515 | protein binding | IPI | 17466626 | |
Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0000718 | nucleotide-excision repair, DNA damage removal | EXP | 10583946 | |
GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
GO:0006367 | transcription initiation from RNA polymerase II promoter | EXP | 8946909 | |
GO:0006368 | RNA elongation from RNA polymerase II promoter | EXP | 9405375 | |
GO:0006350 | transcription | IEA | - | |
GO:0006281 | DNA repair | TAS | 9118947 | |
Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0005634 | nucleus | IEA | - | |
GO:0005654 | nucleoplasm | EXP | 1939271 |2449431 |8946909 |9512541 |9582279 |9790902 |10214908 |11313499 |12393749 |12646563 | |
GO:0005675 | holo TFIIH complex | TAS | 9118947 |
Section V. Pathway annotation
Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
---|---|---|---|
KEGG BASAL TRANSCRIPTION FACTORS | 36 | 24 | All SZGR 2.0 genes in this pathway |
KEGG NUCLEOTIDE EXCISION REPAIR | 44 | 25 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL I TRANSCRIPTION TERMINATION | 22 | 12 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL I TRANSCRIPTION | 89 | 64 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL II TRANSCRIPTION | 105 | 54 | All SZGR 2.0 genes in this pathway |
REACTOME MRNA CAPPING | 30 | 11 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSCRIPTION COUPLED NER TC NER | 45 | 24 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING | 41 | 21 | All SZGR 2.0 genes in this pathway |
REACTOME MRNA PROCESSING | 161 | 86 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSCRIPTION | 210 | 127 | All SZGR 2.0 genes in this pathway |
REACTOME NUCLEOTIDE EXCISION REPAIR | 51 | 27 | All SZGR 2.0 genes in this pathway |
REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX | 45 | 19 | All SZGR 2.0 genes in this pathway |
REACTOME FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX | 30 | 13 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION | 122 | 80 | All SZGR 2.0 genes in this pathway |
REACTOME DNA REPAIR | 112 | 59 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL II PRE TRANSCRIPTION EVENTS | 61 | 32 | All SZGR 2.0 genes in this pathway |
REACTOME GLOBAL GENOMIC NER GG NER | 35 | 20 | All SZGR 2.0 genes in this pathway |
REACTOME FORMATION OF INCISION COMPLEX IN GG NER | 23 | 11 | All SZGR 2.0 genes in this pathway |
REACTOME HIV INFECTION | 207 | 122 | All SZGR 2.0 genes in this pathway |
REACTOME HIV LIFE CYCLE | 125 | 69 | All SZGR 2.0 genes in this pathway |
REACTOME FORMATION OF THE HIV1 EARLY ELONGATION COMPLEX | 34 | 11 | All SZGR 2.0 genes in this pathway |
REACTOME LATE PHASE OF HIV LIFE CYCLE | 104 | 61 | All SZGR 2.0 genes in this pathway |
REACTOME RNA POL I TRANSCRIPTION INITIATION | 25 | 14 | All SZGR 2.0 genes in this pathway |
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP | 1382 | 904 | All SZGR 2.0 genes in this pathway |
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN | 335 | 193 | All SZGR 2.0 genes in this pathway |
KOKKINAKIS METHIONINE DEPRIVATION 48HR UP | 128 | 95 | All SZGR 2.0 genes in this pathway |
KOKKINAKIS METHIONINE DEPRIVATION 96HR UP | 117 | 84 | All SZGR 2.0 genes in this pathway |
WAKASUGI HAVE ZNF143 BINDING SITES | 58 | 33 | All SZGR 2.0 genes in this pathway |
HUMMERICH SKIN CANCER PROGRESSION DN | 100 | 64 | All SZGR 2.0 genes in this pathway |
PUJANA BRCA1 PCC NETWORK | 1652 | 1023 | All SZGR 2.0 genes in this pathway |
PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
PUJANA CHEK2 PCC NETWORK | 779 | 480 | All SZGR 2.0 genes in this pathway |
BENPORATH ES CORE NINE CORRELATED | 100 | 68 | All SZGR 2.0 genes in this pathway |
KAUFFMANN DNA REPAIR GENES | 230 | 137 | All SZGR 2.0 genes in this pathway |
GENTILE UV LOW DOSE UP | 27 | 19 | All SZGR 2.0 genes in this pathway |
ZHANG RESPONSE TO CANTHARIDIN DN | 69 | 46 | All SZGR 2.0 genes in this pathway |
ACEVEDO LIVER CANCER UP | 973 | 570 | All SZGR 2.0 genes in this pathway |
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP | 863 | 514 | All SZGR 2.0 genes in this pathway |
GRADE COLON CANCER UP | 871 | 505 | All SZGR 2.0 genes in this pathway |
LABBE TGFB1 TARGETS DN | 108 | 64 | All SZGR 2.0 genes in this pathway |
MOOTHA PGC | 420 | 269 | All SZGR 2.0 genes in this pathway |
HINATA NFKB TARGETS FIBROBLAST UP | 84 | 60 | All SZGR 2.0 genes in this pathway |
YAGI AML WITH INV 16 TRANSLOCATION | 422 | 277 | All SZGR 2.0 genes in this pathway |
MIKKELSEN ES ICP WITH H3K4ME3 | 718 | 401 | All SZGR 2.0 genes in this pathway |
MIKKELSEN NPC ICP WITH H3K4ME3 | 445 | 257 | All SZGR 2.0 genes in this pathway |
CHYLA CBFA2T3 TARGETS DN | 242 | 146 | All SZGR 2.0 genes in this pathway |
PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |
ROESSLER LIVER CANCER METASTASIS UP | 107 | 72 | All SZGR 2.0 genes in this pathway |