Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for VAMP2
Basic gene info.Gene symbolVAMP2
Gene namevesicle-associated membrane protein 2 (synaptobrevin 2)
SynonymsSYB2|VAMP-2
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :8062464-8066293
Type of geneprotein-coding
RefGenesNM_014232.2,
Ensembl idENSG00000220205
Descriptionsynaptobrevin 2synaptobrevin-2vesicle associated membrane protein 2vesicle-associated membrane protein 2
Modification date20141207
dbXrefs MIM : 185881
HGNC : HGNC
Ensembl : ENSG00000220205
HPRD : 01717
Vega : OTTHUMG00000150254
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VAMP2
BioGPS: 6844
Gene Expression Atlas: ENSG00000220205
The Human Protein Atlas: ENSG00000220205
PathwayNCI Pathway Interaction Database: VAMP2
KEGG: VAMP2
REACTOME: VAMP2
ConsensusPathDB
Pathway Commons: VAMP2
MetabolismMetaCyc: VAMP2
HUMANCyc: VAMP2
RegulationEnsembl's Regulation: ENSG00000220205
miRBase: chr17 :8,062,464-8,066,293
TargetScan: NM_014232
cisRED: ENSG00000220205
ContextiHOP: VAMP2
cancer metabolism search in PubMed: VAMP2
UCL Cancer Institute: VAMP2
Assigned class in ccmGDBC

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Phenotypic Information for VAMP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: VAMP2
Familial Cancer Database: VAMP2
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: VAMP2
MedGen: VAMP2 (Human Medical Genetics with Condition)
ClinVar: VAMP2
PhenotypeMGI: VAMP2 (International Mouse Phenotyping Consortium)
PhenomicDB: VAMP2

Mutations for VAMP2
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VAMP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE764151STIM1111211141097794109891VAMP21141951780627538062834
BE646088HNRNPD1713648327513983275258VAMP21343391780634528063657
D51537VAMP2912191780655648065692LGALS1220271223807575338075807
BI019526VAMP2331111780662138066292ACTB102208755669315567037
BE219072VAMP2221241780630828063184VAMP21195071780626668063054
AI302145VAMP212351780624738062707C16orf80229430165814875758149306
BE771726VAMP2442451780645048064706TNC2262479117838780117838801
BE272026VAMP211131780638128063924TAF4110631206055101460573216

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=2)		Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=0)		Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr17:8064826-8064826p.G100V1
chr17:8064834-8064834p.I97I1
chr17:8064968-8064968p.S80S1
chr17:8065039-8065039p.D57N1
chr17:8065572-8065572p.D40N1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 2                
# mutation 1 2                
nonsynonymous SNV   1                
synonymous SNV 1 1                
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr17:8064834p.I97I1
chr17:8064968p.S80S1
chr17:8065039p.D57N1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for VAMP2 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for VAMP2

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

C17orf59,CTC1,CAMTA2,CBX7,CHD3,CIRBP,CYB5D2,
FXR2,GHDC,LOC284440,NEURL4,NICN1,NISCH,P4HTM,
RANGRF,SPTBN4,TMEM107,TNFSF12,VAMP2,XPA,ZBTB4		APOM,C4orf27,TMEM243,CCDC28A,CCDC59,COMMD6,CSNK2B,
CTF1,DYNLRB1,EIF2B1,FAM127B,FRG1,GABARAP,KRTCAP2,
LOC90110,LYSMD4,SLC25A28,SYF2,TERF2IP,TUSC1,VAMP2

ASAP3,CBX7,CCPG1,DPYD,GABARAPL1,LGI2,NDEL1,
PAFAH1B1,PALM,PLSCR4,PPM1K,RNF122,RNF144B,SLC9A9,
SMG6,SRPX,SYNE1,SYT15,TNFSF12,VAMP2,ZBTB4		BBS1,MAATS1,CALCOCO1,CAMK2A,EZH1,FOXF1,GDI1,
GREM2,KLC1,LGI3,LOC158696,LOC92973,MAGED4B,MPL,
LINC00087,PBXIP1,SEPT5,VAMP2,ZNF548,ZRANB1,ZSCAN18
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for VAMP2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00126vesicle-associated membrane protein 2 (synaptobrevin 2)approved; nutraceuticalVitamin C
DB00121vesicle-associated membrane protein 2 (synaptobrevin 2)approved; nutraceuticalBiotin
DB00130vesicle-associated membrane protein 2 (synaptobrevin 2)approved; nutraceutical; investigationalL-Glutamine
DB00149vesicle-associated membrane protein 2 (synaptobrevin 2)approved; nutraceuticalL-Leucine
DB00122vesicle-associated membrane protein 2 (synaptobrevin 2)approved; nutraceuticalCholine
DB00988vesicle-associated membrane protein 2 (synaptobrevin 2)approvedDopamine


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Cross referenced IDs for VAMP2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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