Summary ?
GeneID2965
SymbolGTF2H1
SynonymsBTF2|P62|TFB1|TFIIH
Descriptiongeneral transcription factor IIH subunit 1
ReferenceMIM:189972|HGNC:HGNC:4655|Ensembl:ENSG00000110768|HPRD:01807|Vega:OTTHUMG00000167690
Gene typeprotein-coding
Map location11p15.1-p14
Pascal p-value0.352
Sherlock p-value0.677
Fetal beta0.532
eGeneCaudate basal ganglia
Cerebellum
Cortex
Frontal Cortex BA9
Hippocampus
Hypothalamus
Nucleus accumbens basal ganglia
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0312 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6025385chr2055703712GTF2H129650.04trans

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
SERTAD40.820.63
LAMC20.820.58
FOXO10.810.34
TSPAN90.800.56
FAM40B0.800.17
FOXP10.790.78
NCOA10.790.78
P2RY10.780.15
RYBP0.770.83
C13orf290.760.32
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FXYD1-0.45-0.67
AF347015.31-0.44-0.66
MT-CO2-0.44-0.68
HIGD1B-0.43-0.67
AF347015.33-0.43-0.63
COPZ2-0.42-0.63
AF347015.8-0.42-0.65
AC021016.1-0.42-0.66
MT-CYB-0.42-0.63
AF347015.2-0.42-0.64

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI8652557 
GO:0008353RNA polymerase subunit kinase activityTAS7533895 
GO:0016251general RNA polymerase II transcription factor activityTAS9118947 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000079regulation of cyclin-dependent protein kinase activityTAS7533895 
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 
GO:0045944positive regulation of transcription from RNA polymerase II promoterIDA8692841 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005654nucleoplasmEXP1939271 |2449431 |8946909 
|9512541 |9582279 
|9790902 |10214908 
|11313499 |12393749 
|12646563 
GO:0005675holo TFIIH complexTAS9118947 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ARAIS | DHTR | HUMARA | KD | NR3C4 | SBMA | SMAX1 | TFMandrogen receptor-HPRD,BioGRID10734072 |11266437 
ATF7IPFLJ10139 | FLJ10688 | MCAF | p621activating transcription factor 7 interacting protein-HPRD10777215 
CCNHCAK | p34 | p37cyclin H-HPRD,BioGRID7533895 
CDK7CAK1 | CDKN7 | MO15 | STK1 | p39MO15cyclin-dependent kinase 7-HPRD,BioGRID9130708 
E2F1E2F-1 | RBAP1 | RBBP3 | RBP3E2F transcription factor 1-HPRD,BioGRID10428966 
ERCC2COFS2 | EM9 | MGC102762 | MGC126218 | MGC126219 | TTD | XPDexcision repair cross-complementing rodent repair deficiency, complementation group 2Affinity Capture-Western
Reconstituted Complex
BioGRID8152490 |9130708 
ERCC3BTF2 | GTF2H | RAD25 | TFIIH | XPBexcision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)Affinity Capture-Western
Co-purification
BioGRID9118947 |9130708 
|15220921 
ERCC3BTF2 | GTF2H | RAD25 | TFIIH | XPBexcision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)-HPRD8194528 |9118947 
ERCC5COFS3 | ERCM2 | UVDR | XPG | XPGCexcision repair cross-complementing rodent repair deficiency, complementation group 5-HPRD8652557 
ESR1DKFZp686N23123 | ER | ESR | ESRA | Era | NR3A1estrogen receptor 1-HPRD,BioGRID10949034 
FUBP1FBP | FUBPfar upstream element (FUSE) binding protein 1-HPRD,BioGRID11239393 
GTF2E1FE | TF2E1 | TFIIE-Ageneral transcription factor IIE, polypeptide 1, alpha 56kDa-HPRD11113176 
HNRNPUHNRPU | SAF-A | U21.1heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)-HPRD10490622 
KIAA1128FLJ14262 | FLJ25809 | Gcap14 | bA486O22.1KIAA1128Two-hybridBioGRID16169070 
KIF13AFLJ27232 | bA500C11.2kinesin family member 13A-HPRD10777215 
MMS19FLJ34167 | FLJ95146 | MET18 | MGC99604 | MMS19L | hMMS19MMS19 nucleotide excision repair homolog (S. cerevisiae)-HPRD11071939 
PLCG1PLC-II | PLC1 | PLC148 | PLCgamma1phospholipase C, gamma 1-HPRD10467411 
POLR2AMGC75453 | POLR2 | POLRA | RPB1 | RPBh1 | RPO2 | RPOL2 | RpIILS | hRPB220 | hsRPB1polymerase (RNA) II (DNA directed) polypeptide A, 220kDa-HPRD9710619 
PSMC2MGC3004 | MSS1 | Nbla10058 | S7proteasome (prosome, macropain) 26S subunit, ATPase, 2-HPRD,BioGRID11118327 
TCEA1GTF2S | SII | TCEA | TF2S | TFIIStranscription elongation factor A (SII), 1Reconstituted ComplexBioGRID9305922 |9765293 
TP53FLJ92943 | LFS1 | TRP53 | p53tumor protein p53-HPRD,BioGRID7935417 


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
GARY CD5 TARGETS DN 431263All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
AMUNDSON RESPONSE TO ARSENITE 217143All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
WANG HCP PROSTATE CANCER 11169All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP 811508All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
NADLER HYPERGLYCEMIA AT OBESITY 5835All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
TAKAO RESPONSE TO UVB RADIATION DN 9867All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS UP 7757All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN 271175All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953554All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN 1011592All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393244All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING DN 4531All SZGR 2.0 genes in this pathway
HOFFMANN PRE BI TO LARGE PRE BII LYMPHOCYTE DN 7561All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP 11687All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES 462273All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1 467251All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP 10772All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-104514581A,m8hsa-miR-10aUACCCUGUAGAUCCGAAUUUGUG
hsa-miR-10bUACCCUGUAGAACCGAAUUUGU
miR-148/1526686751A,m8hsa-miR-148aUCAGUGCACUACAGAACUUUGU
hsa-miR-152brainUCAGUGCAUGACAGAACUUGGG
hsa-miR-148bUCAGUGCAUCACAGAACUUUGU
miR-191531591Ahsa-miR-19aUGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19bUGUGCAAAUCCAUGCAAAACUGA
miR-30-5p300306m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-3308348411A,m8hsa-miR-330brainGCAAAGCACACGGCCUGCAGAGA
miR-3637948001Ahsa-miR-363AUUGCACGGUAUCCAUCUGUAA
miR-3783163221Ahsa-miR-378CUCCUGACUCCAGGUCCUGUGU