Gene Page:VPS35

Summary?
GeneID 55737
Symbol VPS35
Synonyms MEM3|PARK17
Description VPS35, retromer complex component
Reference MIM:601501|HGNC:HGNC:13487|HPRD:06085|
Gene type protein-coding
Map location 16q12
Pascal p-value 0.02
Sherlock p-value 0.36
eGene Myers' cis & trans
Support G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
CompositeSet

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
GSMA_IIE Genome scan meta-analysis (European-ancestry samples) Psr: 0.01775

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs10994209 chr10 61877705 VPS35 55737 0.14 trans

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
Gene Pearson's Correlation Spearman's Correlation
LRRC56 0.62 0.58
CSPG5 0.58 0.61
SCARF2 0.56 0.53
AC011495.3 0.56 0.57
PAK6 0.55 0.55
KIFC2 0.54 0.53
EHBP1L1 0.54 0.58
KIF12 0.54 0.52
CCDC106 0.53 0.51
TFR2 0.52 0.54
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
PELI2 -0.31 -0.14
SOX5 -0.31 -0.13
RBPSUH -0.30 -0.25
NFIB -0.30 -0.16
CBLB -0.29 -0.09
XPR1 -0.29 -0.10
RNF182 -0.29 -0.21
TGFBR1 -0.29 -0.17
PLAG1 -0.29 -0.23
LRCH1 -0.29 -0.13

Section III. Gene Ontology annotation

Molecular function 去term Evidence Neuro keywords PubMed ID
GO:0005515 protein binding 新闻学会 11102511
Biological process 去term Evidence Neuro keywords PubMed ID
GO:0015031 protein transport IEA -
GO:0042147 retrograde transport, endosome to Golgi NAS 11102511
Cellular component 去term Evidence Neuro keywords PubMed ID
GO:0005829 cytosol IDA 11102511
GO:0005737 cytoplasm IEA -
GO:0005768 endosome IDA 11256614
GO:0016020 membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP 408 247 All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL UP 94 59 All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485 293 All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE UP 423 283 All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536 332 All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633 376 All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722 443 All SZGR 2.0 genes in this pathway
ROYLANCE BREAST CANCER 16Q COPY NUMBER UP 63 44 All SZGR 2.0 genes in this pathway
兰斯乳腺癌16问若以桑不光要拷贝数DN 26 19 All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988 594 All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734 436 All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN 517 309 All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882 572 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM 302 191 All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728 415 All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469 239 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973 570 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863 514 All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871 505 All SZGR 2.0 genes in this pathway
CHNG MULTIPLE MYELOMA HYPERPLOID DN 28 19 All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518 299 All SZGR 2.0 genes in this pathway
KUROKAWA LIVER CANCER EARLY RECURRENCE DN 7 6 All SZGR 2.0 genes in this pathway
NAKAYAMA FGF2 TARGETS 29 17 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 1972 1213 All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824 528 All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784 464 All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE 227 151 All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS 220 133 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-124/506 80 86 m8 hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC