Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 CSPG4
Basic gene info.Gene symbolCSPG4
Gene namechondroitin sulfate proteoglycan 4
SynonymsHMW-MAA|MCSP|MCSPG|MEL-CSPG|MSK16|NG2
CytomapUCSC genome browser: 15q24.2
Genomic locationchr15 :75966662-76005189
Type of geneprotein-coding
RefGenesNM_001897.4,
Ensembl idENSG00000173546
Descriptionchondroitin sulfate proteoglycan 4 (melanoma-associated)chondroitin sulfate proteoglycan NG2melanoma chondroitin sulfate proteoglycanmelanoma-associated chondroitin sulfate proteoglycan
Modification date20141207
dbXrefs MIM : 601172
HGNC : HGNC
Ensembl : ENSG00000173546
HPRD : 03105
Vega : OTTHUMG00000142836
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CSPG4
BioGPS: 1464
Gene Expression Atlas: ENSG00000173546
The Human Protein Atlas: ENSG00000173546
PathwayNCI Pathway Interaction Database: CSPG4
KEGG: CSPG4
REACTOME: CSPG4
ConsensusPathDB
Pathway Commons: CSPG4
MetabolismMetaCyc: CSPG4
HUMANCyc: CSPG4
RegulationEnsembl's Regulation: ENSG00000173546
miRBase: chr15 :75,966,662-76,005,189
TargetScan: NM_001897
cisRED: ENSG00000173546
ContextiHOP: CSPG4
cancer metabolism search in PubMed: CSPG4
UCL Cancer Institute: CSPG4
Assigned class in ccmGDBC

Top
Phenotypic Information for CSPG4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CSPG4
Familial Cancer Database: CSPG4
* 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
Orphanet
DiseaseKEGG Disease: CSPG4
MedGen: CSPG4 (Human Medical Genetics with Condition)
ClinVar: CSPG4
PhenotypeMGI: CSPG4 (International Mouse Phenotyping Consortium)
PhenomicDB: CSPG4

Mutations for CSPG4
* 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 CSPG4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD172355CSPG41508157597707675977889SON506806213494561234948153

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)1                
LOSS (# sample)                 
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)

Top
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=6

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=133)
Stat. for Synonymous SNVs
(# total SNVs=74)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr15:75982085-75982085p.E441K6
chr15:75968836-75968836p.G2008G3
chr15:75982428-75982428p.G326G3
chr15:75982058-75982058p.R450W3
chr15:75982072-75982072p.A445V3
chr15:75968309-75968309p.T2184M3
chr15:75981507-75981507p.G633G3
chr15:75982239-75982239p.D389D3
chr15:75968340-75968340p.A2174P3
chr15:75981976-75981976p.R477H3

Top
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
# sample3121154 6 5112353 31418118
# mutation3122184 6 5112673 31624123
nonsynonymous SNV251113 3 4111732 2717114
synonymous SNV17171 3 1  941 197 9
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])

Top
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
chr15:75968313p.G2008G2
chr15:75968836p.D498E2
chr15:75981912p.T2252M2
chr15:75968548p.T102M2
chr15:75982632p.V1197I2
chr15:75983101p.R2183W2
chr15:75968105p.P2104P2
chr15:75979817p.G258G2
chr15:75982567p.R864C1
chr15:75974676p.A2070V1

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 CSPG4 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]

Top
Gene Expression for CSPG4

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ARL10,CHST3,CMTM5,COL4A2,CSPG4,EVX2,EXTL1,
EVA1A,FAM19A3,GPX6,HAPLN4,LIX1,MFGE8,NRXN2,
PMP2,RLBP1,SHC4,SOX6,TIAM2,TRPV4,UBL4B
ABHD15,ACACB,AFAP1L1,AGPAT2,ALDH1L1,AQP7P1,C14orf180,
CAMK1,CEBPA,CIDEC,COL4A2,CSPG4,ITGA7,LIPE,
MLXIPL,PC,PKDCC,PLA2G16,PNPLA2,RXRA,TMEM132C

ARHGEF17,CNTNAP1,CSPG4,CXorf36,DAAM2,DIXDC1,EHD2,
FAM129A,FILIP1,GJC1,HSPG2,ITGB3,JPH2,KIAA1462,
MAP1A,MAP1B,MCAM,MMRN2,MRVI1,MSRB3,TGFB1I1
ADARB1,AHNAK2,COL4A1,CSPG4,DCHS1,DMD,DOCK3,
EHD2,EVC,FRMPD4,FYCO1,GLI2,LAMA5,LAMB2,
MAP4,NBEA,POU3F4,PRICKLE2,RNF150,RYR3,TEAD1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for CSPG4


There's no related Drug.
Top
Cross referenced IDs for CSPG4
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas