Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 VCAN
Basic gene info.Gene symbolVCAN
Gene nameversican
SynonymsCSPG2|ERVR|GHAP|PG-M|WGN|WGN1
CytomapUCSC genome browser: 5q14.3
Genomic locationchr5 :82767492-82878122
Type of geneprotein-coding
RefGenesNM_001126336.2,
NM_001164097.1,NM_001164098.1,NM_004385.4,
Ensembl idENSG00000038427
Descriptionchondroitin sulfate proteoglycan 2chondroitin sulfate proteoglycan core protein 2glial hyaluronate-binding proteinlarge fibroblast proteoglycanversican core proteinversican proteoglycan
Modification date20141222
dbXrefs MIM : 118661
HGNC : HGNC
Ensembl : ENSG00000038427
HPRD : 00340
Vega : OTTHUMG00000131321
ProteinUniProt: P13611
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VCAN
BioGPS: 1462
Gene Expression Atlas: ENSG00000038427
The Human Protein Atlas: ENSG00000038427
PathwayNCI Pathway Interaction Database: VCAN
KEGG: VCAN
REACTOME: VCAN
ConsensusPathDB
Pathway Commons: VCAN
MetabolismMetaCyc: VCAN
HUMANCyc: VCAN
RegulationEnsembl's Regulation: ENSG00000038427
miRBase: chr5 :82,767,492-82,878,122
TargetScan: NM_001126336
cisRED: ENSG00000038427
ContextiHOP: VCAN
cancer metabolism search in PubMed: VCAN
UCL Cancer Institute: VCAN
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for VCAN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: VCAN
Familial Cancer Database: VCAN
* 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_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 118661; gene.
143200; phenotype.
Orphanet 898; Wagner disease.
DiseaseKEGG Disease: VCAN
MedGen: VCAN (Human Medical Genetics with Condition)
ClinVar: VCAN
PhenotypeMGI: VCAN (International Mouse Phenotyping Consortium)
PhenomicDB: VCAN

Mutations for VCAN
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryVCANchr58287320682873226VCANchr58287328482873304
pancreasVCANchr58276938382769403VCANchr58276947782769497
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows VCAN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP392190LGMN1113149317615493178052VCAN11350158287674882877136
AA234873VCAN120558281467482814878ST6GALNAC2200483177456213374563598

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             11  
GAIN (# sample)             1   
LOSS (# sample)              1  
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=401)
Stat. for Synonymous SNVs
(# total SNVs=116)
Stat. for Deletions
(# total SNVs=8)
Stat. for Insertions
(# total SNVs=4)

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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
chr5:82815203-82815203p.A360T4
chr5:82834109-82834109p.T1763A3
chr5:82875963-82875963p.K3349E3
chr5:82836376-82836376p.G2518G3
chr5:82817419-82817419p.I1098M3
chr5:82817231-82817231p.P1036S3
chr5:82817499-82817499p.R1125H3
chr5:82834217-82834217p.L1799L3
chr5:82836059-82836059p.E2413K3
chr5:82837997-82837997p.P3059S2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1110 514 15 1022542112123236131
# mutation1310 904 15 1022712712124753171
nonsynonymous SNV98 633 14 62160237113135153
synonymous SNV42 271 1 4 11145 11618 18
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
chr5:82834217p.L812L,VCAN3
chr5:82815203p.R1125H,VCAN3
chr5:82817499p.A360T,VCAN3
chr5:82836624p.R396H,VCAN2
chr5:82833200p.G290S,VCAN2
chr5:82818051p.F456L,VCAN2
chr5:82876228p.S1189Y,VCAN2
chr5:82816658p.E1541Q,VCAN2
chr5:82875806p.E473K,VCAN2
chr5:82837712p.R648Q,VCAN2

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 VCAN 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 VCAN

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

ADAM12,BNC2,C14orf37,CDH11,COL5A2,COL6A3,DACT1,
FAM26E,FAP,FBN1,GXYLT2,HMCN1,LUM,MXRA5,
NID1,NID2,RECK,ST6GAL2,THBS2,VCAN,ZEB1
ADAMTS6,ARSB,BCAT1,CALU,COL6A3,DCLK1,DNM1,
EMILIN2,FBN1,FN1,FSTL1,GAS7,GFPT2,GPX8,
HMCN1,ITGB3,LGI2,LPAR1,SLC36A1,TRAM2,VCAN

ADAM12,ANTXR1,BGN,COL1A1,COL1A2,COL3A1,COL5A1,
COL5A2,COL6A3,COL8A1,FBN1,FSTL1,GPC6,MRC2,
PDGFRB,SPARC,SULF1,THBS2,VCAN,VGLL3,WISP1
ATP8B2,BGN,CHRD,CHST3,COL5A2,COL6A3,FBN1,
GPR116,HIP1,HMCN1,KIRREL,LAMC1,LDLRAD3,MCC,
PCDHGC3,PDGFRB,RPS6KA2,SH3PXD2B,THSD7A,TMTC1,VCAN
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 VCAN


There's no related Drug.
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Cross referenced IDs for VCAN
* 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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