SZGR2

Summary ?

GeneID	2965
Symbol	GTF2H1
Synonyms	BTF2\|P62\|TFB1\|TFIIH
Description	general transcription factor IIH subunit 1
Reference	MIM:189972\|HGNC:HGNC:4655\|Ensembl:ENSG00000110768\|HPRD:01807\|Vega:OTTHUMG00000167690
Gene type	protein-coding
Map location	11p15.1-p14
Pascal p-value	0.352
Sherlock p-value	0.677
Fetal beta	0.532
eGene	Caudate 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 set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0312

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs6025385	chr20	55703712	GTF2H1	2965		0.04		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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
SERTAD4	0.82	0.63
LAMC2	0.82	0.58
FOXO1	0.81	0.34
TSPAN9	0.80	0.56
FAM40B	0.80	0.17
FOXP1	0.79	0.78
NCOA1	0.79	0.78
P2RY1	0.78	0.15
RYBP	0.77	0.83
C13orf29	0.76	0.32

Top 10 negatively co-expressed genes
Gene	Pearson'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 function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		8652557
GO:0008353	RNA polymerase subunit kinase activity	TAS		7533895
GO:0016251	general RNA polymerase II transcription factor activity	TAS		9118947
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000079	regulation of cyclin-dependent protein kinase activity	TAS		7533895
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
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IDA		8692841
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 IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
AR	AIS \| DHTR \| HUMARA \| KD \| NR3C4 \| SBMA \| SMAX1 \| TFM	androgen receptor	-	HPRD,BioGRID	10734072 \|11266437
ATF7IP	FLJ10139 \| FLJ10688 \| MCAF \| p621	activating transcription factor 7 interacting protein	-	HPRD	10777215
CCNH	CAK \| p34 \| p37	cyclin H	-	HPRD,BioGRID	7533895
CDK7	CAK1 \| CDKN7 \| MO15 \| STK1 \| p39MO15	cyclin-dependent kinase 7	-	HPRD,BioGRID	9130708
E2F1	E2F-1 \| RBAP1 \| RBBP3 \| RBP3	E2F transcription factor 1	-	HPRD,BioGRID	10428966
ERCC2	COFS2 \| EM9 \| MGC102762 \| MGC126218 \| MGC126219 \| TTD \| XPD	excision repair cross-complementing rodent repair deficiency, complementation group 2	Affinity Capture-Western Reconstituted Complex	BioGRID	8152490 \|9130708
ERCC3	BTF2 \| GTF2H \| RAD25 \| TFIIH \| XPB	excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)	Affinity Capture-Western Co-purification	BioGRID	9118947 \|9130708 \|15220921
ERCC3	BTF2 \| GTF2H \| RAD25 \| TFIIH \| XPB	excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)	-	HPRD	8194528 \|9118947
ERCC5	COFS3 \| ERCM2 \| UVDR \| XPG \| XPGC	excision repair cross-complementing rodent repair deficiency, complementation group 5	-	HPRD	8652557
ESR1	DKFZp686N23123 \| ER \| ESR \| ESRA \| Era \| NR3A1	estrogen receptor 1	-	HPRD,BioGRID	10949034
FUBP1	FBP \| FUBP	far upstream element (FUSE) binding protein 1	-	HPRD,BioGRID	11239393
GTF2E1	FE \| TF2E1 \| TFIIE-A	general transcription factor IIE, polypeptide 1, alpha 56kDa	-	HPRD	11113176
HNRNPU	HNRPU \| SAF-A \| U21.1	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	-	HPRD	10490622
KIAA1128	FLJ14262 \| FLJ25809 \| Gcap14 \| bA486O22.1	KIAA1128	Two-hybrid	BioGRID	16169070
KIF13A	FLJ27232 \| bA500C11.2	kinesin family member 13A	-	HPRD	10777215
MMS19	FLJ34167 \| FLJ95146 \| MET18 \| MGC99604 \| MMS19L \| hMMS19	MMS19 nucleotide excision repair homolog (S. cerevisiae)	-	HPRD	11071939
PLCG1	PLC-II \| PLC1 \| PLC148 \| PLCgamma1	phospholipase C, gamma 1	-	HPRD	10467411
POLR2A	MGC75453 \| POLR2 \| POLRA \| RPB1 \| RPBh1 \| RPO2 \| RPOL2 \| RpIILS \| hRPB220 \| hsRPB1	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	-	HPRD	9710619
PSMC2	MGC3004 \| MSS1 \| Nbla10058 \| S7	proteasome (prosome, macropain) 26S subunit, ATPase, 2	-	HPRD,BioGRID	11118327
TCEA1	GTF2S \| SII \| TCEA \| TF2S \| TFIIS	transcription elongation factor A (SII), 1	Reconstituted Complex	BioGRID	9305922 \|9765293
TP53	FLJ92943 \| LFS1 \| TRP53 \| p53	tumor protein p53	-	HPRD,BioGRID	7935417

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
GARY CD5 TARGETS DN	431	263	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
AMUNDSON RESPONSE TO ARSENITE	217	143	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP	414	287	All SZGR 2.0 genes in this pathway
WANG HCP PROSTATE CANCER	111	69	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES	230	137	All SZGR 2.0 genes in this pathway
NADLER HYPERGLYCEMIA AT OBESITY	58	35	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
TAKAO RESPONSE TO UVB RADIATION DN	98	67	All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS UP	77	57	All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN	271	175	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP	953	554	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP	393	244	All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING DN	45	31	All SZGR 2.0 genes in this pathway
HOFFMANN PRE BI TO LARGE PRE BII LYMPHOCYTE DN	75	61	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES	462	273	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP	107	72	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-10	451	458	1A,m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	451	458	1A,m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-148/152	668	675	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-19	153	159	1A	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	153	159	1A	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-30-5p	300	306	m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-330	834	841	1A,m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-363	794	800	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-378	316	322	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: GTF2H1