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 GPC6
Basic gene info.Gene symbolGPC6
Gene nameglypican 6
SynonymsOMIMD1
CytomapUCSC genome browser: 13q32
Genomic locationchr13 :93879077-95060273
Type of geneprotein-coding
RefGenesNM_005708.3,
Ensembl idENSG00000183098
Descriptionglypican proteoglycan 6glypican-6
Modification date20141207
dbXrefs MIM : 604404
HGNC : HGNC
Ensembl : ENSG00000183098
HPRD : 05099
Vega : OTTHUMG00000017205
ProteinUniProt: Q9Y625
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPC6
BioGPS: 10082
Gene Expression Atlas: ENSG00000183098
The Human Protein Atlas: ENSG00000183098
PathwayNCI Pathway Interaction Database: GPC6
KEGG: GPC6
REACTOME: GPC6
ConsensusPathDB
Pathway Commons: GPC6
MetabolismMetaCyc: GPC6
HUMANCyc: GPC6
RegulationEnsembl's Regulation: ENSG00000183098
miRBase: chr13 :93,879,077-95,060,273
TargetScan: NM_005708
cisRED: ENSG00000183098
ContextiHOP: GPC6
cancer metabolism search in PubMed: GPC6
UCL Cancer Institute: GPC6
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GPC6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPC6
Familial Cancer Database: GPC6
* 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 COAD 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 258315; phenotype.
604404; gene.
Orphanet 93329; Autosomal recessive omodysplasia.
DiseaseKEGG Disease: GPC6
MedGen: GPC6 (Human Medical Genetics with Condition)
ClinVar: GPC6
PhenotypeMGI: GPC6 (International Mouse Phenotyping Consortium)
PhenomicDB: GPC6

Mutations for GPC6
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
central_nervous_systemGPC6chr139438177494381774chr139559463095594630
central_nervous_systemGPC6chr139440869994408699GPC6chr139439060794390607
central_nervous_systemGPC6chr139457393394573933chr184729441647294416
central_nervous_systemGPC6chr139457404294574042chr138611307586113075
central_nervous_systemGPC6chr139460770994607709chr181961826719618267
central_nervous_systemGPC6chr139462776594627765GPC6chr139462784694627846
haematopoietic_and_lymphoid_tissueGPC6chr139392312193923121FAM135Achr67115372771153727
liverGPC6chr139483107994831079GPC6chr139501868795018687
liverGPC6chr139499259694992596GPC6chr139501549495015494
ovaryGPC6chr139393640193936421GPC6chr139393135193931371
ovaryGPC6chr139411855294118572URI1chr193047772430477744
ovaryGPC6chr139424918394249203GPC6chr139422568794225707
ovaryGPC6chr139444164994441669NALCN-AS1chr13101383200101383220
ovaryGPC6chr139448139794481417GPC6chr139464555994645579
ovaryGPC6chr139459959394599613GPC6chr139459967094599690
ovaryGPC6chr139488048594880505GPC6chr139496793594967955
pancreasGPC6chr139397317793973197GPC6chr139410859994108619
pancreasGPC6chr139402806594028085chr139387106093871080
pancreasGPC6chr139407729294077312GPC6chr139435688894356908
pancreasGPC6chr139413978994139809GPC6chr139408605194086071
pancreasGPC6chr139479679094796810GPC6chr139487818194878201
pancreasGPC6chr139492596694925986GPC6chr139496835594968375
pancreasGPC6chr139505544095055460chr139506050895060528
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 GPC6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF669457GPC61373139425476994255143GPC6373642139425066094250938
DA568128GPC61336139392696093927295GPC6328816139390646293906949
BF155598GPC638118139444495994445040MPHOSPH8114224132022132120221432

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 # sample124132122 11 11 15124
GAIN (# sample)5  21 20 6 4 131 3
LOSS (# sample)7411112 5 7  2 21
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=77)
Stat. for Synonymous SNVs
(# total SNVs=22)
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
chr13:94197638-94197638p.R95S4
chr13:94482727-94482727p.A214T3
chr13:95050858-95050858p.N476N2
chr13:94197591-94197591p.S79N2
chr13:94482577-94482577p.F164L2
chr13:94482694-94482694p.V203M2
chr13:93879803-93879803p.E32K2
chr13:95034749-95034749p.V412M2
chr13:94680032-94680032p.C254F2
chr13:94938667-94938667p.P314P2

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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
# sample44 181 3 21 1421 1121318
# mutation44 171 3 21 1421 1121419
nonsynonymous SNV44 151 2 11 1021 171315
synonymous SNV   2  1 1  4    51 4
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
chr13:94482724p.R95C2
chr13:93879740p.R213S2
chr13:94482727p.P11S2
chr13:94482577p.A214T2
chr13:94197591p.F164I2
chr13:94958355p.A377E2
chr13:94197638p.V203M2
chr13:94482694p.S79N2
chr13:94197666p.G425R1
chr13:94958286p.H536H1

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 GPC6 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 GPC6

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

ADAMTS2,ANTXR1,BICC1,BNC2,C14orf37,CDH11,COL5A2,
COL6A3,DACT1,DPYSL3,FAP,FBN1,FN1,GPC6,
LOX,MXRA5,NID1,NID2,THBS2,TIMP2,VCAN
ACO1,ALDH2,PQLC2L,CALB2,CIDEC,ESYT1,FAH,
FAM89A,FERMT2,GPC6,GPD1,HEPACAM,HEPN1,LIPE,
MDFIC,MARC1,NPR1,PLIN1,PTGER3,SLC25A16,TSPAN3

ANGPTL2,ANTXR1,BICC1,VSTM4,COL1A2,COL3A1,COL5A2,
COL6A3,DCN,DSEL,FBN1,FSTL1,GPC6,MCC,
PDGFRB,SPARC,SULF1,TIMP2,VCAN,WISP1,ZNF521
ATP1B2,C11orf95,DCLK1,DSEL,EBF3,EFS,FKBP10,
GPC6,HTRA1,JAM2,NAV3,NFIA,NLGN2,NLGN3,
OLFML1,PCDHGA11,PCDHGC3,SLC16A2,STXBP1,TGFBR3,TMTC1
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 GPC6


There's no related Drug.
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Cross referenced IDs for GPC6
* 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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