SZGR2

Summary ?

GeneID	7428
Symbol	VHL
Synonyms	HRCA1\|RCA1\|VHL1\|pVHL
Description	von Hippel-Lindau tumor suppressor
Reference	MIM:608537\|HGNC:HGNC:12687\|HPRD:01905\|
Gene type	protein-coding
Map location	3p25.3
Pascal p-value	0.169
Sherlock p-value	0.878
Fetal beta	1.691
eGene	Myers' cis & trans Meta

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: 0.1204

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10497672		0	VHL	7428		0.17		trans
rs11230726	chr11	61275103	VHL	7428		0.13		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
AC009041.1	0.70	0.53
TRIM17	0.69	0.79
AC009041.3	0.66	0.50
CORT	0.65	0.73
NPAS2	0.65	0.73
TTC22	0.65	0.69
TNK1	0.64	0.24
ANKRD55	0.63	0.77
FHOD1	0.63	0.54
APITD1	0.63	0.73

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HEBP2	-0.36	-0.61
CSRP2	-0.32	-0.48
METRNL	-0.31	-0.47
COTL1	-0.31	-0.25
SNX7	-0.31	-0.26
RNF182	-0.31	-0.37
CBS	-0.30	-0.32
NEUROD6	-0.30	-0.17
SLA	-0.30	-0.11
KLHL1	-0.30	-0.10

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008134	transcription factor binding	TAS		7660122
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	TAS		7660122
GO:0000902	cell morphogenesis	NAS		12169691
GO:0001525	angiogenesis	IEA		-
GO:0006508	proteolysis	TAS		10353251
GO:0006511	ubiquitin-dependent protein catabolic process	IEA		-
GO:0006950	response to stress	NAS		12169691
GO:0008285	negative regulation of cell proliferation	TAS		7660130
GO:0006916	anti-apoptosis	NAS		12169691
GO:0016567	protein ubiquitination	IMP		12169691
GO:0050821	protein stabilization	NAS		12169691
GO:0030163	protein catabolic process	IEA		-
GO:0030198	extracellular matrix organization	IEA		-
GO:0045786	negative regulation of cell cycle	IEA		-
GO:0043534	blood vessel endothelial cell migration	IEA		-
GO:0045597	positive regulation of cell differentiation	NAS		12169691
GO:0045449	regulation of transcription	IMP		15824735
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	TAS		7604013
GO:0005634	nucleus	TAS		7604013
GO:0005737	cytoplasm	IEA		-
GO:0005739	mitochondrion	NAS		12169691
GO:0005783	endoplasmic reticulum	NAS		12169691
GO:0016020	membrane	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
APRT	AMP \| DKFZp686D13177 \| MGC125856 \| MGC125857 \| MGC129961	adenine phosphoribosyltransferase	Affinity Capture-MS	BioGRID	17353931
ATXN2	ATX2 \| FLJ46772 \| SCA2 \| TNRC13	ataxin 2	Affinity Capture-MS	BioGRID	17353931
CAB39	CGI-66 \| FLJ22682 \| MO25	calcium binding protein 39	Affinity Capture-MS	BioGRID	17353931
CCDC59	BR22 \| DKFZp686K1021 \| FLJ10294 \| HSPC128 \| TAP26	coiled-coil domain containing 59	Affinity Capture-MS	BioGRID	17353931
CCDC82	FLJ23518 \| HSPC048	coiled-coil domain containing 82	Affinity Capture-MS	BioGRID	17353931
CDK2	p33(CDK2)	cyclin-dependent kinase 2	Affinity Capture-MS	BioGRID	17353931
CDO1	-	cysteine dioxygenase, type I	Affinity Capture-MS	BioGRID	17353931
CHMP2B	CHMP2.5 \| DKFZp564O123 \| DMT1 \| VPS2-2 \| VPS2B	chromatin modifying protein 2B	Affinity Capture-MS	BioGRID	17353931
CNTF	HCNTF	ciliary neurotrophic factor	Affinity Capture-MS	BioGRID	17353931
CSTB	CST6 \| EPM1 \| PME \| STFB	cystatin B (stefin B)	Affinity Capture-MS	BioGRID	17353931
CSTF3	CSTF-77 \| MGC117398 \| MGC43001 \| MGC75122	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	Affinity Capture-MS	BioGRID	17353931
CUL2	MGC131970	cullin 2	Affinity Capture-MS Affinity Capture-Western Reconstituted Complex	BioGRID	10587522 \|11384984 \|17353931
CUL5	VACM-1 \| VACM1	cullin 5	Reconstituted Complex	BioGRID	11384984
EPAS1	ECYT4 \| HIF2A \| HLF \| MOP2 \| PASD2	endothelial PAS domain protein 1	The von Hippel-Lindau tumor suppressor protein (pVHL) interacts with Hypoxia inducible factor-2-alpha (HIF-2 alpha)	BIND	10823831
FLNA	ABP-280 \| ABPX \| DKFZp434P031 \| FLN \| FLN1 \| FMD \| MNS \| NHBP \| OPD \| OPD1 \| OPD2	filamin A, alpha (actin binding protein 280)	The von Hippel-Lindau tumor suppressor protein (pVHL) interacts with FLNA .	BIND	12169691
FLNA	ABP-280 \| ABPX \| DKFZp434P031 \| FLN \| FLN1 \| FMD \| MNS \| NHBP \| OPD \| OPD1 \| OPD2	filamin A, alpha (actin binding protein 280)	-	HPRD,BioGRID	8674032 \|12169691
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	pVHL interacts with fibronectin 1	BIND	10823831
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	-	HPRD,BioGRID	9651579
FSCN1	FLJ38511 \| SNL \| p55	fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)	Affinity Capture-MS	BioGRID	17353931
HAS1	HAS	hyaluronan synthase 1	Affinity Capture-MS	BioGRID	17353931
HDAC1	DKFZp686H12203 \| GON-10 \| HD1 \| RPD3 \| RPD3L1	histone deacetylase 1	Reconstituted Complex	BioGRID	11641274
HDAC2	RPD3 \| YAF1	histone deacetylase 2	Reconstituted Complex	BioGRID	11641274
HDAC3	HD3 \| RPD3 \| RPD3-2	histone deacetylase 3	Reconstituted Complex	BioGRID	11641274
HIF1A	HIF-1alpha \| HIF1 \| HIF1-ALPHA \| MOP1 \| PASD8	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	Hydroxylated HIF-1 alpha interacts with VHL. This interaction was modeled on a demonstrated interaction between human hydroxylated HIF-1 alpha and an unspecified isoform of VHL from an unspecified species.	BIND	15721254
HIF1A	HIF-1alpha \| HIF1 \| HIF1-ALPHA \| MOP1 \| PASD8	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	The von Hippel-Lindau tumor suppressor protein (pVHL) interacts with Hypoxia inducible factor-alpha (HIF-1 alpha)	BIND	10823831
HIF1A	HIF-1alpha \| HIF1 \| HIF1-ALPHA \| MOP1 \| PASD8	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	-	HPRD	11504942
HIF1A	HIF-1alpha \| HIF1 \| HIF1-ALPHA \| MOP1 \| PASD8	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	HIF1A (HIF-1alpha) interacts with VHL.	BIND	15750626
HIF1A	HIF-1alpha \| HIF1 \| HIF1-ALPHA \| MOP1 \| PASD8	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	-	HPRD,BioGRID	10944113
HIF1AN	DKFZp762F1811 \| FIH1 \| FLJ20615 \| FLJ22027	hypoxia-inducible factor 1, alpha subunit inhibitor	Reconstituted Complex	BioGRID	11641274
HIF3A	HIF-3A \| HIF-3A2 \| HIF-3A4 \| IPAS \| MOP7 \| PASD7 \| bHLHe17	hypoxia inducible factor 3, alpha subunit	-	HPRD	12538644
HIST1H2BC	H2B.1 \| H2B/l \| H2BFL \| MGC104246 \| dJ221C16.3	histone cluster 1, H2bc	Affinity Capture-MS	BioGRID	17353931
HNRNPA2B1	DKFZp779B0244 \| FLJ22720 \| HNRNPA2 \| HNRNPB1 \| HNRPA2 \| HNRPA2B1 \| HNRPB1 \| RNPA2 \| SNRPB1	heterogeneous nuclear ribonucleoprotein A2/B1	-	HPRD,BioGRID	11517223
IARS	FLJ20736 \| IARS1 \| ILRS \| PRO0785	isoleucyl-tRNA synthetase	Affinity Capture-MS	BioGRID	17353931
IMPDH2	IMPD2 \| IMPDH-II	IMP (inosine monophosphate) dehydrogenase 2	Affinity Capture-MS	BioGRID	17353931
JMJD1C	DKFZp761F0118 \| FLJ14374 \| KIAA1380 \| RP11-10C13.2 \| TRIP8	jumonji domain containing 1C	Affinity Capture-MS	BioGRID	17353931
KNTC1	FLJ36151 \| KIAA0166 \| ROD	kinetochore associated 1	Affinity Capture-MS	BioGRID	17353931
MCC	DKFZp762O1615 \| FLJ38893 \| FLJ46755 \| MCC1	mutated in colorectal cancers	Affinity Capture-MS	BioGRID	17353931
MOBKL3	2C4D \| CGI-95 \| MGC12264 \| MOB1 \| MOB3 \| PREI3	MOB1, Mps One Binder kinase activator-like 3 (yeast)	Affinity Capture-MS	BioGRID	17353931
MRCL3	MLCB \| MRLC3	myosin regulatory light chain MRCL3	Affinity Capture-MS	BioGRID	17353931
NEDD8	FLJ43224 \| MGC104393 \| MGC125896 \| MGC125897 \| Nedd-8	neural precursor cell expressed, developmentally down-regulated 8	Affinity Capture-MS	BioGRID	17353931
PAPSS2	ATPSK2 \| SK2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	Affinity Capture-MS	BioGRID	17353931
PCMT1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase	Affinity Capture-MS	BioGRID	17353931
PFAS	FGAMS \| FGARAT \| KIAA0361 \| PURL	phosphoribosylformylglycinamidine synthase	Affinity Capture-MS	BioGRID	17353931
PHF17	FLJ22479 \| JADE1 \| KIAA1807	PHD finger protein 17	The von Hippel-Lindau tumor suppressor protein (pVHL) interacts with Jade-1	BIND	12169691
PHF17	FLJ22479 \| JADE1 \| KIAA1807	PHD finger protein 17	-	HPRD,BioGRID	12169691
PIN1	DOD \| UBL5	peptidylprolyl cis/trans isomerase, NIMA-interacting 1	Affinity Capture-MS	BioGRID	17353931
PKD1L3	-	polycystic kidney disease 1-like 3	Affinity Capture-MS	BioGRID	17353931
PPIB	CYP-S1 \| CYPB \| MGC14109 \| MGC2224 \| SCYLP	peptidylprolyl isomerase B (cyclophilin B)	Affinity Capture-MS	BioGRID	17353931
PSMB1	FLJ25321 \| HC5 \| KIAA1838 \| PMSB1 \| PSC5	proteasome (prosome, macropain) subunit, beta type, 1	Affinity Capture-MS	BioGRID	17353931
PSMB3	HC10-II \| MGC4147	proteasome (prosome, macropain) subunit, beta type, 3	Affinity Capture-MS	BioGRID	17353931
PSMC3	MGC8487 \| TBP1	proteasome (prosome, macropain) 26S subunit, ATPase, 3	-	HPRD,BioGRID	14556007
PSMD13	HSPC027 \| Rpn9 \| S11 \| p40.5	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	Affinity Capture-MS	BioGRID	17353931
RAB1B	-	RAB1B, member RAS oncogene family	Affinity Capture-MS	BioGRID	17353931
RASGRP1	CALDAG-GEFI \| CALDAG-GEFII \| MGC129998 \| MGC129999 \| RASGRP \| V \| hRasGRP1	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	Affinity Capture-MS	BioGRID	17353931
RBX1	BA554C12.1 \| MGC13357 \| MGC1481 \| RNF75 \| ROC1	ring-box 1	Affinity Capture-MS	BioGRID	17353931
RHOC	ARH9 \| ARHC \| H9 \| MGC1448 \| MGC61427 \| RHOH9	ras homolog gene family, member C	Affinity Capture-MS	BioGRID	17353931
RNF139	HRCA1 \| MGC31961 \| RCA1 \| TRC8	ring finger protein 139	-	HPRD	12032852
RPA3	REPA3	replication protein A3, 14kDa	Affinity Capture-MS	BioGRID	17353931
RPS9	-	ribosomal protein S9	Affinity Capture-MS	BioGRID	17353931
STK16	FLJ39635 \| KRCT \| MPSK \| PKL12 \| TSF1	serine/threonine kinase 16	Affinity Capture-MS	BioGRID	17353931
TAGLN2	HA1756 \| KIAA0120	transgelin 2	Affinity Capture-MS	BioGRID	17353931
TARS	MGC9344 \| ThrRS	threonyl-tRNA synthetase	Affinity Capture-MS	BioGRID	17353931
TCEB1	SIII	transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)	Affinity Capture-MS Co-crystal Structure Reconstituted Complex Two-hybrid	BioGRID	8674032 \|10587522 \|11739384 \|12004076 \|17353931
TCEB1	SIII	transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)	-	HPRD	7660130 \|10449727 \|12004076
TCEB2	ELOB \| SIII	transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)	Affinity Capture-MS Affinity Capture-Western Co-crystal Structure Reconstituted Complex	BioGRID	10587522 \|12004076 \|17353931
TGFB1I1	ARA55 \| HIC-5 \| HIC5 \| TSC-5	transforming growth factor beta 1 induced transcript 1	Affinity Capture-MS	BioGRID	17353931
TPT1	FLJ27337 \| HRF \| TCTP \| p02	tumor protein, translationally-controlled 1	Affinity Capture-MS	BioGRID	17353931
TRIM28	FLJ29029 \| KAP1 \| RNF96 \| TF1B \| TIF1B	tripartite motif-containing 28	Reconstituted Complex	BioGRID	12682018
TXN	DKFZp686B1993 \| MGC61975 \| TRX \| TRX1	thioredoxin	Affinity Capture-MS	BioGRID	17353931
USP33	KIAA1097 \| MGC16868 \| VDU1	ubiquitin specific peptidase 33	pVHL interacts with VDU1-type II.	BIND	11739384
USP33	KIAA1097 \| MGC16868 \| VDU1	ubiquitin specific peptidase 33	-	HPRD,BioGRID	11739384
VBP1	PFD3 \| PFDN3 \| VBP-1	von Hippel-Lindau binding protein 1	Affinity Capture-Western Two-hybrid	BioGRID	8674032 \|12169691
VBP1	PFD3 \| PFDN3 \| VBP-1	von Hippel-Lindau binding protein 1	The von Hippel-Lindau tumor suppressor protein (pVHL) interacts with VBP1.	BIND	12169691
ZNF197	D3S1363E \| P18 \| VHLaK \| ZKSCAN9 \| ZNF166 \| ZNF20	zinc finger protein 197	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	12682018

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG UBIQUITIN MEDIATED PROTEOLYSIS	138	98	All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER	328	259	All SZGR 2.0 genes in this pathway
KEGG RENAL CELL CARCINOMA	70	60	All SZGR 2.0 genes in this pathway
BIOCARTA HIF PATHWAY	15	12	All SZGR 2.0 genes in this pathway
BIOCARTA VEGF PATHWAY	29	18	All SZGR 2.0 genes in this pathway
PID HIF2PATHWAY	34	29	All SZGR 2.0 genes in this pathway
PID HIF1A PATHWAY	19	12	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN	25	17	All SZGR 2.0 genes in this pathway
REACTOME OXYGEN DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA INDUCIBLE FACTOR ALPHA	18	12	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME ADAPTIVE IMMUNE SYSTEM	539	350	All SZGR 2.0 genes in this pathway
REACTOME CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION	251	156	All SZGR 2.0 genes in this pathway
REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	212	129	All SZGR 2.0 genes in this pathway
NOJIMA SFRP2 TARGETS UP	31	23	All SZGR 2.0 genes in this pathway
DARWICHE SKIN TUMOR PROMOTER DN	185	115	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK LOW DN	165	107	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH UP	147	101	All SZGR 2.0 genes in this pathway
DARWICHE SQUAMOUS CELL CARCINOMA UP	146	104	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN	800	473	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 5	147	89	All SZGR 2.0 genes in this pathway
HERNANDEZ ABERRANT MITOSIS BY DOCETACEL 2NM UP	81	57	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH VS LOW UP	6	6	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
GROSS HYPOXIA VIA HIF1A DN	110	78	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 AND HIF1A UP	142	104	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX	230	156	All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC	182	116	All SZGR 2.0 genes in this pathway
DORSAM HOXA9 TARGETS DN	32	22	All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP	323	240	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
DANG MYC TARGETS DN	31	25	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
QI HYPOXIA	140	96	All SZGR 2.0 genes in this pathway

Gene Page: VHL