Gene Page:VPS52
Summary?
| GeneID | 6293 |
| Symbol | VPS52 |
| Synonyms | ARE1|SAC2|SACM2L|dJ1033B10.5 |
| Description | VPS52, GARP complex subunit |
| Reference | MIM:603443|HGNC:HGNC:10518|Ensembl:ENSG00000223501|HPRD:09142|Vega:OTTHUMG00000031276 |
| Gene type | protein-coding |
| Map location | 6p21.3 |
| Pascal p-value | 3.235E-5 |
| Sherlock p-value | 0.014 |
| Fetal beta | -0.599 |
| DMG | 2 (# studies) |
| Support | G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Jaffe_2016 | Genome-wide DNA methylation analysis | This 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_2016 | Genome-wide DNA methylation analysis | This dataset includes 172 replicated associations between CpGs with schizophrenia. | 2 |
| GSMA_I | Genome scan meta-analysis | Psr: 0.033 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg03078690 | 6 | 33235504 | VPS52 | 2.97E-5 | 0.006 | 0.074 | DMG:Montano_2016 |
| cg19277288 | 6 | 33216268 | VPS52 | 7.97E-8 | -0.009 | 1.87E-5 | DMG:Jaffe_2016 |
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 |
| DAAM1 | 0.93 | 0.96 |
| TDG | 0.92 | 0.94 |
| RSG17 | 0.92 | 0.94 |
| HMGCR | 0.92 | 0.96 |
| ANKRD50 | 0.91 | 0.95 |
| LPHN3 | 0.91 | 0.92 |
| C6orf174 | 0.90 | 0.95 |
| B4GALT5 | 0.90 | 0.95 |
| PANX1 | 0.90 | 0.95 |
| BIVM | 0.90 | 0.94 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson'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 process | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0015031 | protein transport | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005794 | Golgi apparatus | IEA | - | |
| GO:0005768 | endosome | IEA | - | |
| GO:0016020 | membrane | IEA | - | |
| GO:0010008 | endosome membrane | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| BOGNI TREATMENT RELATED MYELOID LEUKEMIA DN | 33 | 19 | All SZGR 2.0 genes in this pathway |
| VANHARANTA UTERINE FIBROID WITH 7Q DELETION DN | 36 | 23 | All SZGR 2.0 genes in this pathway |
| BENPORATH NANOG TARGETS | 988 | 594 | All SZGR 2.0 genes in this pathway |
| BENPORATH OCT4 TARGETS | 290 | 172 | All SZGR 2.0 genes in this pathway |
| BENPORATH SOX2 TARGETS | 734 | 436 | All SZGR 2.0 genes in this pathway |
| BENPORATH NOS TARGETS | 179 | 105 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| PETRETTO HEART MASS QTL CIS UP | 28 | 15 | All SZGR 2.0 genes in this pathway |
| BYSTRYKH HEMATOPOIESIS STEM CELL QTL CIS | 128 | 77 | All SZGR 2.0 genes in this pathway |
| CHESLER BRAIN QTL CIS | 75 | 51 | All SZGR 2.0 genes in this pathway |
| BYSTRYKH造血干细胞和大脑QTL CIS | 65 | 38 | All SZGR 2.0 genes in this pathway |
| CHESLER BRAIN HIGHEST GENETIC VARIANCE | 37 | 21 | All SZGR 2.0 genes in this pathway |
| JISON SICKLE CELL DISEASE DN | 181 | 97 | All SZGR 2.0 genes in this pathway |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |
| KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP | 756 | 494 | All SZGR 2.0 genes in this pathway |
| KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP | 682 | 440 | All SZGR 2.0 genes in this pathway |
| FIGUEROA AML METHYLATION CLUSTER 1 DN | 48 | 30 | All SZGR 2.0 genes in this pathway |
| FEVR CTNNB1 TARGETS UP | 682 | 433 | All SZGR 2.0 genes in this pathway |
| VANOEVELEN MYOGENESIS SIN3A TARGETS | 220 | 133 | All SZGR 2.0 genes in this pathway |