Gene Page: VPS11

Summary ?
GeneID55823
SymbolVPS11
SynonymsEND1|HLD12|PEP5|RNF108|hVPS11
DescriptionVPS11, CORVET/HOPS core subunit
ReferenceMIM:608549|HGNC:HGNC:14583|Ensembl:ENSG00000160695|HPRD:12258|Vega:OTTHUMG00000166355
Gene typeprotein-coding
Map location11q23
Pascal p-value0.014
Sherlock p-value0.872
eGeneCaudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Hypothalamus
Nucleus accumbens basal ganglia
Putamen basal ganglia
Myers' cis & trans
Meta
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
GSMA_IGenome scan meta-analysisPsr: 0.006 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs538478chr11118925340VPS11558230.14cis
rs1786141chr11118938314VPS11558230.14cis
rs2508948chr11118951641VPS11558230.12cis
rs4614chr11118952370VPS11558230.16cis
rs494048chr11118961230VPS11558230.09cis
rs12052673chr214325550VPS11558230.16trans
rs100308111118913993VPS11ENSG00000160695.107.875E-80-24410gtex_brain_putamen_basal
rs50135111118917814VPS11ENSG00000160695.102.31E-60-20589gtex_brain_putamen_basal
rs1121713311118928249VPS11ENSG00000160695.104.867E-70-10154gtex_brain_putamen_basal
rs250912111118928253VPS11ENSG00000160695.103.908E-70-10150gtex_brain_putamen_basal
rs1121713711118931030VPS11ENSG00000160695.104.311E-70-7373gtex_brain_putamen_basal
rs20151337611118935420VPS11ENSG00000160695.104.517E-70-2983gtex_brain_putamen_basal
rs792510011118941596VPS11ENSG00000160695.104.901E-703193gtex_brain_putamen_basal
rs1089232811118942654VPS11ENSG00000160695.104.697E-704251gtex_brain_putamen_basal
rs382506111118944675VPS11ENSG00000160695.104.748E-706272gtex_brain_putamen_basal
rs15051442511118946251VPS11ENSG00000160695.101.383E-707848gtex_brain_putamen_basal
rs117756211118949331VPS11ENSG00000160695.101.813E-7010928gtex_brain_putamen_basal
rs250894811118951642VPS11ENSG00000160695.101.416E-6013239gtex_brain_putamen_basal
rs1581811118952173VPS11ENSG00000160695.102.571E-6013770gtex_brain_putamen_basal
rs461411118952371VPS11ENSG00000160695.102.581E-6013968gtex_brain_putamen_basal
rs792438711118954265VPS11ENSG00000160695.101.301E-6015862gtex_brain_putamen_basal
rs59219011118955314VPS11ENSG00000160695.102.274E-6016911gtex_brain_putamen_basal
rs58992511118955679VPS11ENSG00000160695.102.48E-6017276gtex_brain_putamen_basal
rs179999211118957246VPS11ENSG00000160695.101.24E-6018843gtex_brain_putamen_basal
rs1121714811118957735VPS11ENSG00000160695.102.493E-6019332gtex_brain_putamen_basal
rs47420111118958229VPS11ENSG00000160695.102.394E-6019826gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
RWDD2A0.830.79
UBE2E10.810.78
KLHDC20.790.77
EIF1B0.790.78
MRPS350.780.75
ACTR100.780.71
HACL10.780.75
ORC5L0.780.75
CIRH1A0.780.76
NUPL20.780.73
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.18-0.62-0.66
AF347015.26-0.62-0.59
MT-CO2-0.61-0.53
AF347015.8-0.60-0.56
AF347015.2-0.60-0.54
MT-CYB-0.60-0.54
AF347015.15-0.57-0.53
AF347015.31-0.56-0.51
AF347015.21-0.56-0.49
AC098691.2-0.56-0.60

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0000166nucleotide bindingIEA-
GO:0005515protein bindingIPI15231747 
GO:0005524ATP bindingIEA-
GO:0008270zinc ion bindingIEA-
GO:0046872metal ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0015031protein transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005765lysosomal membraneIEA-
GO:0005769early endosomeIEA-
GO:0016020membraneIEA-
GO:0005884actin filamentIEA-
GO:0031902late endosome membraneIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
BCAR1CAS | CAS1 | CASS1 | CRKAS | P130Casbreast cancer anti-estrogen resistance 1Two-hybridBioGRID16169070 
LSM1CASM | YJL124CLSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)Two-hybridBioGRID15231747 
MARK3CTAK1 | KP78 | PAR1AMAP/microtubule affinity-regulating kinase 3Two-hybridBioGRID16169070 
STX1AHPC-1 | STX1 | p35-1syntaxin 1A (brain)VPS11 interacts with STX1A (Syntaxin-1). This interaction was modeled on a demonstrated interaction between human VPS11 and STX1A (Syntaxin-1) from an unspecified species.BIND14623309 
STX6-syntaxin 6Vps11 interacts with Stx6 (Syntaxin-6). This interaction was modeled on a demonstrated interaction between human Vps11 and Stx6 (Syntaxin-6) from an unspecified species.BIND14623309 
STX7-syntaxin 7VPS11 interacts with STX7 (Syntaxin-7). This interaction was modeled on a demonstrated interaction between human VPS11 and STX7 (Syntaxin-7) from an unspecified species.BIND14623309 
STX7-syntaxin 7-HPRD,BioGRID11382755 
STX8CARBsyntaxin 8VPS11 interacts with STX8 (Syntaxin-8). This interaction was modeled on a demonstrated interaction between human VPS11 and STX8 (Syntaxin-8) from an unspecified species.BIND14623309 
VPS16hVPS16vacuolar protein sorting 16 homolog (S. cerevisiae)-HPRD,BioGRID11382755 
VPS18KIAA1475 | PEP3vacuolar protein sorting 18 homolog (S. cerevisiae)-HPRD,BioGRID11382755 
VPS33AFLJ22395 | FLJ23187vacuolar protein sorting 33 homolog A (S. cerevisiae)-HPRD,BioGRID11382755 
VPS45H1 | H1VPS45 | VPS45A | VPS45B | VPS54A | VSP45 | VSP45Avacuolar protein sorting 45 homolog (S. cerevisiae)VPS11 interacts with VPS45A (VPS45). This interaction was modeled on a demonstrated interaction between human VPS11 and rat VPS45.BIND14623309 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP 1821933All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479299All SZGR 2.0 genes in this pathway
LEE LIVER CANCER ACOX1 DN 6539All SZGR 2.0 genes in this pathway
YAGI AML SURVIVAL 12987All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469239All SZGR 2.0 genes in this pathway
MCCABE HOXC6 TARGETS CANCER UP 3123All SZGR 2.0 genes in this pathway
WINTER HYPOXIA METAGENE 242168All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway