SZGR2

Summary ?

GeneID	6844
Symbol	VAMP2
Synonyms	SYB2\|VAMP-2
Description	vesicle associated membrane protein 2
Reference	MIM:185881\|HGNC:HGNC:12643\|Ensembl:ENSG00000220205\|HPRD:01717\|Vega:OTTHUMG00000150254
Gene type	protein-coding
Map location	17p13.1
Pascal p-value	0.361
Sherlock p-value	0.801
DEG p-value	DEG:Maycox_2009:CC_BA10_fold_change=-1.11:CC_BA10_disease_P=0.0403:HBB_BA9_fold_change=-1.28:HBB_BA9_disease_P=0.0379
Fetal beta	-1.939
Support	EXOCYTOSIS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_mGluR5 G2Cdb.human_TAP-PSD-95-CORE CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
DEG:Maycox_2009	Microarray to determine the expression of over 30000 mRNA transcripts in post-mortem tissue	We included 51 genes whose expression changes are common between two schizophrenia cohorts.
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,schizophrenic,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

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
DNAJC28	0.74	0.69
FBXO9	0.73	0.64
TTC35	0.69	0.67
C2orf74	0.69	0.61
KRT222P	0.68	0.58
NMNAT1	0.68	0.70
C13orf1	0.68	0.59
C1D	0.67	0.60
SGTB	0.66	0.56
TYW3	0.66	0.57

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HYAL2	-0.44	-0.44
OLFM2	-0.41	-0.38
SEMA4B	-0.40	-0.35
SH3BP2	-0.39	-0.39
AC006276.1	-0.39	-0.34
NAPRT1	-0.39	-0.33
SH2B2	-0.39	-0.41
SPNS1	-0.38	-0.32
SLC38A5	-0.38	-0.40
WDR86	-0.38	-0.37

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:0016020	membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		1976629
GO:0030054	cell junction	IEA		-
GO:0031410	cytoplasmic vesicle	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BCAP31	6C6-AG \| BAP31 \| CDM \| DXS1357E	B-cell receptor-associated protein 31	Reconstituted Complex	BioGRID	9396746
CPLX1	CPX-I \| CPX1	complexin 1	-	HPRD,BioGRID	11832227
DNAJC5	CSP \| DKFZp434N1429 \| DKFZp761N1221 \| DNAJC5A \| FLJ00118 \| FLJ13070	DnaJ (Hsp40) homolog, subfamily C, member 5	Csp1 interacts with VAMP2. This interaction was modeled on a demonstrated interaction between cow Csp1, and human VAMP2.	BIND	15610015
NAPA	SNAPA	N-ethylmaleimide-sensitive factor attachment protein, alpha	Reconstituted Complex	BioGRID	7622514
RABAC1	PRA1 \| PRAF1 \| YIP3	Rab acceptor 1 (prenylated)	-	HPRD,BioGRID	9341137
SNAP23	HsT17016 \| SNAP23A \| SNAP23B	synaptosomal-associated protein, 23kDa	SNAP23 interacts with VAMP2.	BIND	15610015
SNAP23	HsT17016 \| SNAP23A \| SNAP23B	synaptosomal-associated protein, 23kDa	-	HPRD,BioGRID	10713150
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	-	HPRD	7961655
SNAP25	FLJ23079 \| RIC-4 \| RIC4 \| SEC9 \| SNAP \| SNAP-25 \| bA416N4.2 \| dJ1068F16.2	synaptosomal-associated protein, 25kDa	Affinity Capture-Western Co-crystal Structure Far Western Reconstituted Complex Two-hybrid	BioGRID	9030619 \|11524423 \|11832227
STX11	FHL4 \| HLH4 \| HPLH4	syntaxin 11	-	HPRD,BioGRID	10036234
STX1A	HPC-1 \| STX1 \| p35-1	syntaxin 1A (brain)	Affinity Capture-Western Co-crystal Structure Far Western Reconstituted Complex Two-hybrid	BioGRID	7553862 \|9030619 \|10100611 \|10449403 \|11832227 \|12093152
STX1B	STX1B1 \| STX1B2	syntaxin 1B	-	HPRD,BioGRID	12093152
STX2	EPIM \| EPM \| MGC51014 \| STX2A \| STX2B \| STX2C	syntaxin 2	Two-hybrid	BioGRID	12828989
STX3	STX3A	syntaxin 3	Two-hybrid	BioGRID	12828989
STX4	STX4A \| p35-2	syntaxin 4	Affinity Capture-Western Two-hybrid	BioGRID	8760387 \|10194441 \|10820264 \|12517971
STX4	STX4A \| p35-2	syntaxin 4	-	HPRD	8760387 \|12417022 \|12517971\|8770861
STXBP2	Hunc18b \| MUNC18-2 \| UNC18-2 \| UNC18B \| pp10122	syntaxin binding protein 2	-	HPRD	12773094
STXBP3	MUNC18-3 \| MUNC18C \| PSP \| UNC-18C	syntaxin binding protein 3	Reconstituted Complex	BioGRID	12832401
SYPL1	H-SP1 \| SYPL	synaptophysin-like 1	-	HPRD	10370136
TRPC3	TRP3	transient receptor potential cation channel, subfamily C, member 3	-	HPRD	15327778
TRPC3	TRP3	transient receptor potential cation channel, subfamily C, member 3	TRPC3 interacts with VAMP2.	BIND	15327778
UNC13B	MGC133279 \| MGC133280 \| MUNC13 \| UNC13 \| Unc13h2 \| hmunc13	unc-13 homolog B (C. elegans)	Co-fractionation	BioGRID	8999968
VAMP3	CEB	vesicle-associated membrane protein 3 (cellubrevin)	Reconstituted Complex	BioGRID	12130530
VAMP8	EDB	vesicle-associated membrane protein 8 (endobrevin)	Reconstituted Complex	BioGRID	12130530
VAPA	MGC3745 \| VAP-33 \| VAP-A \| VAP33 \| hVAP-33	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa	-	HPRD,BioGRID	9657962
VAPB	ALS8 \| VAMP-B \| VAMP-C \| VAP-B \| VAP-C	VAMP (vesicle-associated membrane protein)-associated protein B and C	-	HPRD,BioGRID	9920726

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
KEGG VASOPRESSIN REGULATED WATER REABSORPTION	44	30	All SZGR 2.0 genes in this pathway
PID INSULIN GLUCOSE PATHWAY	26	24	All SZGR 2.0 genes in this pathway
REACTOME MEMBRANE TRAFFICKING	129	74	All SZGR 2.0 genes in this pathway
REACTOME BOTULINUM NEUROTOXICITY	19	14	All SZGR 2.0 genes in this pathway
REACTOME TRANS GOLGI NETWORK VESICLE BUDDING	60	31	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 GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE	15	13	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE	34	30	All SZGR 2.0 genes in this pathway
REACTOME INTEGRATION OF ENERGY METABOLISM	120	84	All SZGR 2.0 genes in this pathway
REACTOME DOPAMINE NEUROTRANSMITTER RELEASE CYCLE	11	11	All SZGR 2.0 genes in this pathway
REACTOME ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE	10	9	All SZGR 2.0 genes in this pathway
REACTOME DIABETES PATHWAYS	133	91	All SZGR 2.0 genes in this pathway
REACTOME NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE	10	10	All SZGR 2.0 genes in this pathway
REACTOME INSULIN SYNTHESIS AND PROCESSING	21	15	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF INSULIN SECRETION	93	65	All SZGR 2.0 genes in this pathway
REACTOME LYSOSOME VESICLE BIOGENESIS	23	11	All SZGR 2.0 genes in this pathway
REACTOME GOLGI ASSOCIATED VESICLE BIOGENESIS	53	27	All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION	17	16	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP	473	314	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL UP	276	187	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 5	147	89	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP	479	299	All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX	230	156	All SZGR 2.0 genes in this pathway
STARK HYPPOCAMPUS 22Q11 DELETION UP	53	40	All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN	83	69	All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC	182	116	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL	63	50	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
MCCLUNG COCAINE REWARD 5D	79	62	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
RAMPON ENRICHED LEARNING ENVIRONMENT EARLY UP	15	12	All SZGR 2.0 genes in this pathway
AMBROSINI FLAVOPIRIDOL TREATMENT TP53	109	63	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN	546	362	All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL DN	102	65	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR UP	221	150	All SZGR 2.0 genes in this pathway
STEIN ESR1 TARGETS	85	55	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
ZEMBUTSU SENSITIVITY TO DOXORUBICIN	17	10	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 DN	448	282	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	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-1/206	946	952	m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-127	98	104	m8	hsa-miR-127^brain	UCGGAUCCGUCUGAGCUUGGCU
miR-133	912	918	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	912	918	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-135	70	76	1A	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	70	76	1A	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-150	522	528	m8	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-153	325	332	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-25/32/92/363/367	328	334	1A	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-28	1234	1240	m8	hsa-miR-28^brain	AAGGAGCUCACAGUCUAUUGAG
miR-30-3p	1185	1192	1A,m8	hsa-miR-30a-3p	CUUUCAGUCGGAUGUUUGCAGC
miR-30-3p	1185	1192	1A,m8	hsa-miR-30e-3p	CUUUCAGUCGGAUGUUUACAGC
miR-325	202	208	1A	hsa-miR-325	CCUAGUAGGUGUCCAGUAAGUGU
miR-338	1553	1560	1A,m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-338	1553	1560	1A,m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-34/449	1226	1232	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
				hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
				hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-34b	1100	1106	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-369-3p	169	175	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	169	175	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-377	1534	1540	1A	hsa-miR-377	AUCACACAAAGGCAACUUUUGU
miR-409-5p	1688	1694	1A	hsa-miR-409-5p	AGGUUACCCGAGCAACUUUGCA
miR-410	171	177	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-448	326	332	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-491	1481	1487	1A	hsa-miR-491^brain	AGUGGGGAACCCUUCCAUGAGGA
miR-493-5p	1666	1673	1A,m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU

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: VAMP2