SZGR2

Summary ?

GeneID	6843
Symbol	VAMP1
Synonyms	SPAX1\|SYB1\|VAMP-1
Description	vesicle associated membrane protein 1
Reference	MIM:185880\|HGNC:HGNC:12642\|Ensembl: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	qvalue	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)

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	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		9920726
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016192	vesicle-mediated transport	IEA		-
Cellular component	GO term	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
GAL LEUKEMIC 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
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-15/16/195/424/497	178	184	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: VAMP1