Gene Page: VPS11
Summary ?
GeneID | 55823 |
Symbol | VPS11 |
Synonyms | END1|HLD12|PEP5|RNF108|hVPS11 |
Description | VPS11, CORVET/HOPS core subunit |
Reference | MIM:608549|HGNC:HGNC:14583|Ensembl:ENSG00000160695|HPRD:12258|Vega:OTTHUMG00000166355 |
Gene type | protein-coding |
Map location | 11q23 |
Pascal p-value | 0.014 |
Sherlock p-value | 0.872 |
eGene | Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta |
Support | G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS |
Gene in Data Sources
Gene set name | Method of gene set | Description | Info |
---|---|---|---|
CV:PGCnp | Genome-wide Association Study | GWAS | |
GSMA_I | Genome scan meta-analysis | Psr: 0.006 |
Section I. Genetics and epigenetics annotation
eQTL annotation
SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
---|---|---|---|---|---|---|---|---|
rs538478 | chr11 | 118925340 | VPS11 | 55823 | 0.14 | cis | ||
rs1786141 | chr11 | 118938314 | VPS11 | 55823 | 0.14 | cis | ||
rs2508948 | chr11 | 118951641 | VPS11 | 55823 | 0.12 | cis | ||
rs4614 | chr11 | 118952370 | VPS11 | 55823 | 0.16 | cis | ||
rs494048 | chr11 | 118961230 | VPS11 | 55823 | 0.09 | cis | ||
rs12052673 | chr2 | 14325550 | VPS11 | 55823 | 0.16 | trans | ||
rs1003081 | 11 | 118913993 | VPS11 | ENSG00000160695.10 | 7.875E-8 | 0 | -24410 | gtex_brain_putamen_basal |
rs501351 | 11 | 118917814 | VPS11 | ENSG00000160695.10 | 2.31E-6 | 0 | -20589 | gtex_brain_putamen_basal |
rs11217133 | 11 | 118928249 | VPS11 | ENSG00000160695.10 | 4.867E-7 | 0 | -10154 | gtex_brain_putamen_basal |
rs2509121 | 11 | 118928253 | VPS11 | ENSG00000160695.10 | 3.908E-7 | 0 | -10150 | gtex_brain_putamen_basal |
rs11217137 | 11 | 118931030 | VPS11 | ENSG00000160695.10 | 4.311E-7 | 0 | -7373 | gtex_brain_putamen_basal |
rs201513376 | 11 | 118935420 | VPS11 | ENSG00000160695.10 | 4.517E-7 | 0 | -2983 | gtex_brain_putamen_basal |
rs7925100 | 11 | 118941596 | VPS11 | ENSG00000160695.10 | 4.901E-7 | 0 | 3193 | gtex_brain_putamen_basal |
rs10892328 | 11 | 118942654 | VPS11 | ENSG00000160695.10 | 4.697E-7 | 0 | 4251 | gtex_brain_putamen_basal |
rs3825061 | 11 | 118944675 | VPS11 | ENSG00000160695.10 | 4.748E-7 | 0 | 6272 | gtex_brain_putamen_basal |
rs150514425 | 11 | 118946251 | VPS11 | ENSG00000160695.10 | 1.383E-7 | 0 | 7848 | gtex_brain_putamen_basal |
rs1177562 | 11 | 118949331 | VPS11 | ENSG00000160695.10 | 1.813E-7 | 0 | 10928 | gtex_brain_putamen_basal |
rs2508948 | 11 | 118951642 | VPS11 | ENSG00000160695.10 | 1.416E-6 | 0 | 13239 | gtex_brain_putamen_basal |
rs15818 | 11 | 118952173 | VPS11 | ENSG00000160695.10 | 2.571E-6 | 0 | 13770 | gtex_brain_putamen_basal |
rs4614 | 11 | 118952371 | VPS11 | ENSG00000160695.10 | 2.581E-6 | 0 | 13968 | gtex_brain_putamen_basal |
rs7924387 | 11 | 118954265 | VPS11 | ENSG00000160695.10 | 1.301E-6 | 0 | 15862 | gtex_brain_putamen_basal |
rs592190 | 11 | 118955314 | VPS11 | ENSG00000160695.10 | 2.274E-6 | 0 | 16911 | gtex_brain_putamen_basal |
rs589925 | 11 | 118955679 | VPS11 | ENSG00000160695.10 | 2.48E-6 | 0 | 17276 | gtex_brain_putamen_basal |
rs1799992 | 11 | 118957246 | VPS11 | ENSG00000160695.10 | 1.24E-6 | 0 | 18843 | gtex_brain_putamen_basal |
rs11217148 | 11 | 118957735 | VPS11 | ENSG00000160695.10 | 2.493E-6 | 0 | 19332 | gtex_brain_putamen_basal |
rs474201 | 11 | 118958229 | VPS11 | ENSG00000160695.10 | 2.394E-6 | 0 | 19826 | gtex_brain_putamen_basal |
Section II. Transcriptome annotation
General gene expression (GTEx)

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 |
RWDD2A | 0.83 | 0.79 |
UBE2E1 | 0.81 | 0.78 |
KLHDC2 | 0.79 | 0.77 |
EIF1B | 0.79 | 0.78 |
MRPS35 | 0.78 | 0.75 |
ACTR10 | 0.78 | 0.71 |
HACL1 | 0.78 | 0.75 |
ORC5L | 0.78 | 0.75 |
CIRH1A | 0.78 | 0.76 |
NUPL2 | 0.78 | 0.73 |
Top 10 negatively co-expressed genes | ||
Gene | Pearson'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 function | GO term | Evidence | Neuro keywords | PubMed ID |
---|---|---|---|---|
GO:0000166 | nucleotide binding | IEA | - | |
GO:0005515 | protein binding | IPI | 15231747 | |
GO:0005524 | ATP binding | IEA | - | |
GO:0008270 | zinc ion binding | IEA | - | |
GO:0046872 | metal ion binding | IEA | - | |
Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0015031 | protein transport | IEA | - | |
Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0005765 | lysosomal membrane | IEA | - | |
GO:0005769 | early endosome | IEA | - | |
GO:0016020 | membrane | IEA | - | |
GO:0005884 | actin filament | IEA | - | |
GO:0031902 | late endosome membrane | IEA | - |
Section IV. Protein-protein interaction annotation
Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
---|---|---|---|---|---|
BCAR1 | CAS | CAS1 | CASS1 | CRKAS | P130Cas | breast cancer anti-estrogen resistance 1 | Two-hybrid | BioGRID | 16169070 |
LSM1 | CASM | YJL124C | LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) | Two-hybrid | BioGRID | 15231747 |
MARK3 | CTAK1 | KP78 | PAR1A | MAP/microtubule affinity-regulating kinase 3 | Two-hybrid | BioGRID | 16169070 |
STX1A | HPC-1 | STX1 | p35-1 | syntaxin 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. | BIND | 14623309 |
STX6 | - | syntaxin 6 | Vps11 interacts with Stx6 (Syntaxin-6). This interaction was modeled on a demonstrated interaction between human Vps11 and Stx6 (Syntaxin-6) from an unspecified species. | BIND | 14623309 |
STX7 | - | syntaxin 7 | VPS11 interacts with STX7 (Syntaxin-7). This interaction was modeled on a demonstrated interaction between human VPS11 and STX7 (Syntaxin-7) from an unspecified species. | BIND | 14623309 |
STX7 | - | syntaxin 7 | - | HPRD,BioGRID | 11382755 |
STX8 | CARB | syntaxin 8 | VPS11 interacts with STX8 (Syntaxin-8). This interaction was modeled on a demonstrated interaction between human VPS11 and STX8 (Syntaxin-8) from an unspecified species. | BIND | 14623309 |
VPS16 | hVPS16 | vacuolar protein sorting 16 homolog (S. cerevisiae) | - | HPRD,BioGRID | 11382755 |
VPS18 | KIAA1475 | PEP3 | vacuolar protein sorting 18 homolog (S. cerevisiae) | - | HPRD,BioGRID | 11382755 |
VPS33A | FLJ22395 | FLJ23187 | vacuolar protein sorting 33 homolog A (S. cerevisiae) | - | HPRD,BioGRID | 11382755 |
VPS45 | H1 | H1VPS45 | VPS45A | VPS45B | VPS54A | VSP45 | VSP45A | vacuolar 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. | BIND | 14623309 |
Section V. Pathway annotation
Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
---|---|---|---|
PARENT MTOR SIGNALING UP | 567 | 375 | All SZGR 2.0 genes in this pathway |
DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP | 479 | 299 | All SZGR 2.0 genes in this pathway |
LEE LIVER CANCER ACOX1 DN | 65 | 39 | All SZGR 2.0 genes in this pathway |
YAGI AML SURVIVAL | 129 | 87 | All SZGR 2.0 genes in this pathway |
IVANOVA HEMATOPOIESIS EARLY PROGENITOR | 532 | 309 | All SZGR 2.0 genes in this pathway |
BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
MARSON BOUND BY FOXP3 UNSTIMULATED | 1229 | 713 | All SZGR 2.0 genes in this pathway |
MCCABE BOUND BY HOXC6 | 469 | 239 | All SZGR 2.0 genes in this pathway |
MCCABE HOXC6 TARGETS CANCER UP | 31 | 23 | All SZGR 2.0 genes in this pathway |
WINTER HYPOXIA METAGENE | 242 | 168 | All SZGR 2.0 genes in this pathway |
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | All SZGR 2.0 genes in this pathway |