Gene Page:VAMP1

Summary?
GeneID 6843
Symbol VAMP1
Synonyms SPAX1|SYB1|VAMP-1
Description vesicle associated membrane protein 1
Reference MIM:185880|HGNC: HGNC: 12642|运用:ENSG00000139190|HPRD:01716|Vega:OTTHUMG00000168269
Gene type protein-coding
Map location 12p
Pascal p-value 0.88
Sherlock p-value 0.509
Fetal beta -2.817
DMG 1 (# studies)
eGene Cerebellar Hemisphere
Cerebellum
Myers' cis & trans
Support EXOCYTOSIS
SEROTONIN
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Nishioka_2013 Genome-wide DNA methylation analysis The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenics,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg25750404 12 6579648 VAMP1 -0.022 0.45 DMG:Nishioka_2013

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs10510196 chr3 723427 VAMP1 6843 0.04 trans
rs2131824 chr6 125775939 VAMP1 6843 0.01 trans
rs2248 chr6 125777720 VAMP1 6843 0.01 trans
rs2249 chr6 125777752 VAMP1 6843 0.01 trans
rs1494142 chr6 125778157 VAMP1 6843 0.07 trans
rs1494160 chr6 125784791 VAMP1 6843 0.01 trans
rs1494158 chr6 125785156 VAMP1 6843 0.01 trans
rs10860768 chr12 102069497 VAMP1 6843 0.17 trans
rs6096615 chr20 50472392 VAMP1 6843 0.01 trans
rs16999646 chr21 25544091 VAMP1 6843 0.19 trans
rs16999651 chr21 25544635 VAMP1 6843 0.09 trans
rs10482945 chr21 25544889 VAMP1 6843 0.18 trans
rs8130791 chr21 25545446 VAMP1 6843 0.18 trans
rs7887792 chrX 20508216 VAMP1 6843 0 trans
rs5990879 chrX 20517507 VAMP1 6843 0.01 trans

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
Gene Pearson's Correlation Spearman's Correlation
COPZ1 0.84 0.82
C8orf41 0.83 0.83
DAP3 0.82 0.81
SPG21 0.82 0.81
CNBP 0.82 0.79
CHCHD3 0.81 0.78
PRMT5 0.81 0.77
EIF3I 0.81 0.80
USP39 0.81 0.80
VPS45 0.81 0.80
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.8 -0.69 -0.67
MT-CO2 -0.69 -0.67
AF347015.27 -0.68 -0.68
AF347015.21 -0.66 -0.64
AF347015.2 -0.66 -0.68
MT-CYB -0.66 -0.66
AF347015.15 -0.65 -0.67
AF347015.31 -0.65 -0.66
AF347015.26 -0.64 -0.66
AF347015.33 -0.64 -0.64

Section III. Gene Ontology annotation

Molecular function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005515 protein binding 新闻学会 9920726
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0016192 vesicle-mediated transport IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0019717 synaptosome IEA Synap, Brain (GO term level: 7) -
GO:0045202 synapse IEA neuron, Synap, Neurotransmitter, Glial (GO term level: 2) -
GO:0005739 mitochondrion IEA -
GO:0005741 mitochondrial outer membrane IEA -
GO:0016020 membrane IEA -
GO:0005887 integral to plasma membrane TAS 1976629
GO:0030054 cell junction IEA -
GO:0031410 cytoplasmic vesicle IEA -
GO:0030659 cytoplasmic vesicle membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT 38 25 All SZGR 2.0 genes in this pathway
REACTOME BOTULINUM NEUROTOXICITY 19 14 All SZGR 2.0 genes in this pathway
REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS 17 12 All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279 221 All SZGR 2.0 genes in this pathway
KORKOLA SEMINOMA UP 44 27 All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP 177 110 All SZGR 2.0 genes in this pathway
加白血病STEM CELL DN 244 153 All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER DN 406 230 All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES CD4 DN 116 71 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442 892 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 AND BRAIN QTL TRANS 185 114 All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293 193 All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN 153 120 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237 837 All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP 89 59 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT DN 165 106 All SZGR 2.0 genes in this pathway
BILD MYC ONCOGENIC SIGNATURE 206 117 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476 285 All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN 342 220 All SZGR 2.0 genes in this pathway
LEE DIFFERENTIATING T LYMPHOCYTE 200 115 All SZGR 2.0 genes in this pathway
GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA DN 56 39 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242 146 All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP 279 155 All SZGR 2.0 genes in this pathway
ZWANG DOWN BY 2ND EGF PULSE 293 119 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-15/16/195/424/497 178 184 m8 hsa-miR-15abrain UAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brain UAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrain UAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZ UAGCAGCACAGAAAUAUUGGC
hsa-miR-424 CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497 CAGCAGCACACUGUGGUUUGU