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 GPC5
Basic gene info.Gene symbolGPC5
Gene nameglypican 5
Synonyms-
CytomapUCSC genome browser: 13q32
Genomic locationchr13 :92050934-93519487
Type of geneprotein-coding
RefGenesNM_004466.5,
Ensembl idENSG00000179399
DescriptionbA93M14.1glypican proteoglycan 5glypican-5
Modification date20141207
dbXrefs MIM : 602446
HGNC : HGNC
Ensembl : ENSG00000179399
HPRD : 03902
Vega : OTTHUMG00000017200
ProteinUniProt: P78333
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPC5
BioGPS: 2262
Gene Expression Atlas: ENSG00000179399
The Human Protein Atlas: ENSG00000179399
PathwayNCI Pathway Interaction Database: GPC5
KEGG: GPC5
REACTOME: GPC5
ConsensusPathDB
Pathway Commons: GPC5
MetabolismMetaCyc: GPC5
HUMANCyc: GPC5
RegulationEnsembl's Regulation: ENSG00000179399
miRBase: chr13 :92,050,934-93,519,487
TargetScan: NM_004466
cisRED: ENSG00000179399
ContextiHOP: GPC5
cancer metabolism search in PubMed: GPC5
UCL Cancer Institute: GPC5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GPC5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPC5
Familial Cancer Database: GPC5
* 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 BLCA 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/vaop/ncurrent/full/nature12965.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 602446; gene.
Orphanet
DiseaseKEGG Disease: GPC5
MedGen: GPC5 (Human Medical Genetics with Condition)
ClinVar: GPC5
PhenotypeMGI: GPC5 (International Mouse Phenotyping Consortium)
PhenomicDB: GPC5

Mutations for GPC5
* 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
breastGPC5chr139345009793450097chr8138327667138327667
haematopoietic_and_lymphoid_tissueGPC5chr139268888492688884GPC5chr139268888492688884
haematopoietic_and_lymphoid_tissueGPC5chr139318749893187498GPC5chr139318749893187498
ovaryGPC5chr139222103092221050GPC5chr139214641492146434
ovaryGPC5chr139224822892248248GPC5chr139225018792250207
ovaryGPC5chr139227935592279375chr212541135825411378
ovaryGPC5chr139233236992332389GPC5chr139234789692347916
ovaryGPC5chr139239655192396571GPC5chr139239663092396650
ovaryGPC5chr139262242492622444GPC5chr139262371192623731
ovaryGPC5chr139287988892879908chr117626551376265533
ovaryGPC5chr139302995093029970ASIC2chr173134384931343869
ovaryGPC5chr139314370093143720CADPSchr36275115162751171
ovaryGPC5chr139319094693191146chr69427507394275273
ovaryGPC5chr139330509193305111GPC5chr139330611493306134
pancreasGPC5chr139241007992410099GPC5chr139241428992414309
pancreasGPC5chr139280278192802801GPC5chr139283183292831852
pancreasGPC5chr139280658492806604GPC5chr139295703392957053
pancreasGPC5chr139335620493356224GPC5chr139335631493356334
pancreasGPC5chr139345709893457118GPC5chr139347015893470178
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 GPC5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DW467550GPC517137139347606093476181GPC5138345139347346193473668
DW446998GPC517137139347606093476181GPC5138214139347346193473537
AI827689GPC52414139299205093004461CDYL412501647160284716117

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 # sample73  226 9 3  3422
GAIN (# sample)73  116 5 1  34 2
LOSS (# sample)    11  4 2  1 2 
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=111)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=3)
There's no deleted 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
chr13:92101015-92101015p.G55E4
chr13:93518536-93518536p.W521*3
chr13:92380805-92380805p.R347H3
chr13:92101156-92101156p.R102Q3
chr13:92345629-92345629p.P172S3
chr13:92101100-92101100p.Q83H2
chr13:92345655-92345655p.N180N2
chr13:92346087-92346087p.N324N2
chr13:92345845-92345845p.F244V2
chr13:92380835-92380835p.R357H2

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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
# sample58 131 10 41 16113  2619114
# mutation58 131 11 41 20113  2919118
nonsynonymous SNV45 11  8 41 13113  2313115
synonymous SNV13 21 3    7    66 3
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
chr13:92380805p.R347H3
chr13:92797193p.Q83H2
chr13:92797198p.R217W2
chr13:92345629p.E480K2
chr13:92380859p.R102Q2
chr13:92345744p.P172S2
chr13:92101100p.C504C2
chr13:92345880p.G506V2
chr13:93518546p.E365G2
chr13:92345764p.M255I2

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 GPC5 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 GPC5

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

ATP1A4,ACSM6,C11orf94,MROH7,C2orf27B,CASQ1,CHIA,
DEFB109P1B,GPC5,HERC1,HHEX,KCNJ8,LOC149620,LOC285780,
LOC340508,MS4A8,OR52B4,OR8B8,PROK1,SKINTL,TSPAN6
ADAM22,ADRB3,AFF2,ALDOB,C1orf198,CADM2,CES1P1,
CRIM1,DAAM1,GNAL,GPC5,GPLD1,KIAA0040,NECAB1,
NLGN1,NRCAM,PCLO,PTPRQ,SCIN,TMEM64,YAP1

AKR1C8P,ATP12A,C3P1,CCDC85A,CD7,CELF4,CHST9,
DIO1,FAM138D,FLJ35024,FOXB1,GPC5,GSTA3,HOXC12,
KCNB2,MS4A15,PAK3,RDH8,S100A7A,SERPIND1,SPDYC
CCDC181,CACNG4,CDK5R2,CELF3,CELF6,CPLX2,ELAVL4,
ETV1,GNG3,GPC5,HMP19,OLFM3,PABPC1L2B,PIRT,
RANBP3L,SCG2,SCG3,SLC6A15,SULT4A1,SYT9,UCHL1
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 GPC5


There's no related Drug.
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Cross referenced IDs for GPC5
* 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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