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 GPC3
Basic gene info.Gene symbolGPC3
Gene nameglypican 3
SynonymsDGSX|GTR2-2|MXR7|OCI-5|SDYS|SGB|SGBS|SGBS1
CytomapUCSC genome browser: Xq26.1
Genomic locationchrX :132669775-133119673
Type of geneprotein-coding
RefGenesNM_001164617.1,
NM_001164618.1,NM_001164619.1,NM_004484.3,
Ensembl idENSG00000147257
Descriptionglypican proteoglycan 3glypican-3heparan sulphate proteoglycanintestinal protein OCI-5secreted glypican-3
Modification date20141222
dbXrefs MIM : 300037
HGNC : HGNC
Ensembl : ENSG00000147257
HPRD : 02074
Vega : OTTHUMG00000022448
ProteinUniProt: P51654
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPC3
BioGPS: 2719
Gene Expression Atlas: ENSG00000147257
The Human Protein Atlas: ENSG00000147257
PathwayNCI Pathway Interaction Database: GPC3
KEGG: GPC3
REACTOME: GPC3
ConsensusPathDB
Pathway Commons: GPC3
MetabolismMetaCyc: GPC3
HUMANCyc: GPC3
RegulationEnsembl's Regulation: ENSG00000147257
miRBase: chrX :132,669,775-133,119,673
TargetScan: NM_001164617
cisRED: ENSG00000147257
ContextiHOP: GPC3
cancer metabolism search in PubMed: GPC3
UCL Cancer Institute: GPC3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GPC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPC3
Familial Cancer Database: GPC3
* 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 300037; gene.
312870; phenotype.
Orphanet 373; Simpson-Golabi-Behmel syndrome.
DiseaseKEGG Disease: GPC3
MedGen: GPC3 (Human Medical Genetics with Condition)
ClinVar: GPC3
PhenotypeMGI: GPC3 (International Mouse Phenotyping Consortium)
PhenomicDB: GPC3

Mutations for GPC3
* 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 GPC3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI905820LRPPRC120524420954744223116GPC3204390X132669773132669958
R64084TNKS1317896367909637105GPC3308369X132669781132669842
AI468457GPC34202X132669773132669971PDGFRA19634845516330755163459
BG153241CD74561215149781425149781490GPC3116135X132846201132846220
BC036707TTL13282113260721113289983GPC3317344X132690723132690986

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=61)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr23:132887698-132887698p.V281V2
chr23:133119341-133119341p.Q46*2
chr23:132888051-132888051p.D164H2
chr23:132670253-132670253p.E548K2
chr23:132887945-132887945p.R199Q2
chr23:132730611-132730611p.S477F2
chr23:132887946-132887946p.R199*2
chr23:132887676-132887676p.V289L2
chr23:132730510-132730510p.D511N1
chr23:132888160-132888160p.N127N1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 101 2 2  841  91 10
# mutation11 101 2 2  841  91 14
nonsynonymous SNV11 91   2  431  71 9
synonymous SNV   1  2    41   2  5
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
chrX:132888183p.R145Q,GPC32
chrX:132887945p.R66C,GPC32
chrX:132730611p.S343Y,GPC31
chrX:133087081p.L66I,GPC31
chrX:132887716p.L524L,GPC31
chrX:132887949p.E327D,GPC31
chrX:132670204p.L144F,GPC31
chrX:132730618p.V38V,GPC31
chrX:133087087p.L510R,GPC31
chrX:132887741p.H323R,GPC31

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 GPC3 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 GPC3

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

AFP,C9orf135,CEACAM16,CHRNA6,CNTN4,CRH,CXorf30,
CHDC2,DLX1,DLX2,ENOX1,GHRH,GPC3,HS6ST2,
C7orf62,OPTC,PART1,PLA2G2C,PRSS21,RASSF6,TAF1L
AIDA,ANGPTL2,CELF2,CNRIP1,CRTAP,EBF3,FBLN5,
GPC3,HOXC8,HSD17B11,LAMC1,MXRA7,NEGR1,NPR2,
PCOLCE2,PID1,PMP22,RNASE4,TIMP3,SLC35G2,VIM

ANKRD53,BSX,CADM3,CFC1B,EBF3,GABRG2,GFRA2,
GPC3,GRIA1,KCNS2,KIAA1045,MC4R,NR2E1,OR7E5P,
PM20D1,PYDC2,RSPO1,SLC17A7,TAC3,TNXB,TSHR
ANKRD1,ACTRT3,LINC00323,C2orf69,PXDC1,C8orf22,COLEC11,
DRD5,FAM35A,FAM35DP,FAM35BP,FGF5,FMO3,GPC3,
HAR1B,ITGB8,LOC645166,LOC654342,POPDC3,SLC14A2,TNFRSF12A
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 GPC3


There's no related Drug.
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Cross referenced IDs for GPC3
* 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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