Summary ?
GeneID6843
SymbolVAMP1
SynonymsSPAX1|SYB1|VAMP-1
Descriptionvesicle associated membrane protein 1
ReferenceMIM:185880|HGNC:HGNC:12642|Ensembl:ENSG00000139190|HPRD:01716|Vega:OTTHUMG00000168269
Gene typeprotein-coding
Map location12p
Pascal p-value0.88
Sherlock p-value0.509
Fetal beta-2.817
DMG1 (# studies)
eGeneCerebellar Hemisphere
Cerebellum
Myers' cis & trans
SupportEXOCYTOSIS
SEROTONIN
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe 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:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenics,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg25750404126579648VAMP1-0.0220.45DMG:Nishioka_2013

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10510196chr3723427VAMP168430.04trans
rs2131824chr6125775939VAMP168430.01trans
rs2248chr6125777720VAMP168430.01trans
rs2249chr6125777752VAMP168430.01trans
rs1494142chr6125778157VAMP168430.07trans
rs1494160chr6125784791VAMP168430.01trans
rs1494158chr6125785156VAMP168430.01trans
rs10860768chr12102069497VAMP168430.17trans
rs6096615chr2050472392VAMP168430.01trans
rs16999646chr2125544091VAMP168430.19trans
rs16999651chr2125544635VAMP168430.09trans
rs10482945chr2125544889VAMP168430.18trans
rs8130791chr2125545446VAMP168430.18trans
rs7887792chrX20508216VAMP168430trans
rs5990879chrX20517507VAMP168430.01trans

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
COPZ10.840.82
C8orf410.830.83
DAP30.820.81
SPG210.820.81
CNBP0.820.79
CHCHD30.810.78
PRMT50.810.77
EIF3I0.810.80
USP390.810.80
VPS450.810.80
Top 10 negatively co-expressed genes
GenePearson'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 functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI9920726 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0016192vesicle-mediated transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0019717synaptosomeIEASynap, Brain (GO term level: 7)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0005739mitochondrionIEA-
GO:0005741mitochondrial outer membraneIEA-
GO:0016020membraneIEA-
GO:0005887integral to plasma membraneTAS1976629 
GO:0030054cell junctionIEA-
GO:0031410cytoplasmic vesicleIEA-
GO:0030659cytoplasmic vesicle membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT 3825All SZGR 2.0 genes in this pathway
REACTOME BOTULINUM NEUROTOXICITY 1914All SZGR 2.0 genes in this pathway
REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS 1712All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
KORKOLA SEMINOMA UP 4427All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP 177110All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL DN 244153All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER DN 406230All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES CD4 DN 11671All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All 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 AND BRAIN QTL TRANS 185114All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293193All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN 153120All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP 8959All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT DN 165106All SZGR 2.0 genes in this pathway
BILD MYC ONCOGENIC SIGNATURE 206117All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN 342220All SZGR 2.0 genes in this pathway
LEE DIFFERENTIATING T LYMPHOCYTE 200115All SZGR 2.0 genes in this pathway
GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA DN 5639All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242146All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP 279155All SZGR 2.0 genes in this pathway
ZWANG DOWN BY 2ND EGF PULSE 293119All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-15/16/195/424/497178184m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU