Gene Page: VPS52

Summary ?
GeneID6293
SymbolVPS52
SynonymsARE1|SAC2|SACM2L|dJ1033B10.5
DescriptionVPS52, GARP complex subunit
ReferenceMIM:603443|HGNC:HGNC:10518|Ensembl:ENSG00000223501|HPRD:09142|Vega:OTTHUMG00000031276
Gene typeprotein-coding
Map location6p21.3
Pascal p-value3.235E-5
Sherlock p-value0.014
Fetal beta-0.599
DMG2 (# studies)
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
CompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
DMG:Montano_2016Genome-wide DNA methylation analysisThis dataset includes 172 replicated associations between CpGs with schizophrenia. 2
GSMA_IGenome scan meta-analysisPsr: 0.033 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg03078690633235504VPS522.97E-50.0060.074DMG:Montano_2016
cg19277288633216268VPS527.97E-8-0.0091.87E-5DMG:Jaffe_2016


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
DAAM10.930.96
TDG0.920.94
RSG170.920.94
HMGCR0.920.96
ANKRD500.910.95
LPHN30.910.92
C6orf1740.900.95
B4GALT50.900.95
PANX10.900.95
BIVM0.900.94
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AIFM3-0.70-0.78
TSC22D4-0.70-0.82
HLA-F-0.70-0.79
HEPN1-0.69-0.77
S100B-0.69-0.83
AF347015.31-0.68-0.86
FXYD1-0.68-0.86
HSD17B14-0.68-0.79
MT-CO2-0.68-0.88
AF347015.33-0.67-0.85

Section III. Gene Ontology annotation

Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0015031protein transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005794Golgi apparatusIEA-
GO:0005768endosomeIEA-
GO:0016020membraneIEA-
GO:0010008endosome membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BOGNI TREATMENT RELATED MYELOID LEUKEMIA DN 3319All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID WITH 7Q DELETION DN 3623All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290172All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH NOS TARGETS 179105All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
PETRETTO HEART MASS QTL CIS UP 2815All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL CIS 12877All SZGR 2.0 genes in this pathway
CHESLER BRAIN QTL CIS 7551All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL CIS 6538All SZGR 2.0 genes in this pathway
CHESLER BRAIN HIGHEST GENETIC VARIANCE 3721All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE DN 18197All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756494All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 1 DN 4830All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP 682433All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS 220133All SZGR 2.0 genes in this pathway