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 GSTM5
Basic gene info.Gene symbolGSTM5
Gene nameglutathione S-transferase mu 5
SynonymsGSTM5-5|GTM5
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :110254863-110260890
Type of geneprotein-coding
RefGenesNM_000851.3,
Ensembl idENSG00000134201
DescriptionGST class-mu 5S-(hydroxyalkyl)glutathione lyase M5glutathione S-alkyltransferase M5glutathione S-aralkyltransferase M5glutathione S-aryltransferase M5glutathione S-transferase M5glutathione S-transferase Mu 5
Modification date20141207
dbXrefs MIM : 138385
HGNC : HGNC
Ensembl : ENSG00000134201
HPRD : 00711
Vega : OTTHUMG00000011644
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSTM5
BioGPS: 2949
Gene Expression Atlas: ENSG00000134201
The Human Protein Atlas: ENSG00000134201
PathwayNCI Pathway Interaction Database: GSTM5
KEGG: GSTM5
REACTOME: GSTM5
ConsensusPathDB
Pathway Commons: GSTM5
MetabolismMetaCyc: GSTM5
HUMANCyc: GSTM5
RegulationEnsembl's Regulation: ENSG00000134201
miRBase: chr1 :110,254,863-110,260,890
TargetScan: NM_000851
cisRED: ENSG00000134201
ContextiHOP: GSTM5
cancer metabolism search in PubMed: GSTM5
UCL Cancer Institute: GSTM5
Assigned class in ccmGDBC

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Phenotypic Information for GSTM5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GSTM5
Familial Cancer Database: GSTM5
* 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
KEGG_GLUTATHIONE_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GSTM5
MedGen: GSTM5 (Human Medical Genetics with Condition)
ClinVar: GSTM5
PhenotypeMGI: GSTM5 (International Mouse Phenotyping Consortium)
PhenomicDB: GSTM5

Mutations for GSTM5
* 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 GSTM5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV701798GSTM51891110256149110256332GSTM4844011110199002110201648

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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=34)
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
chr1:110257831-110257831p.L179P11
chr1:110255748-110255748p.D40D9
chr1:110257757-110257757p.T154T5
chr1:110257836-110257836p.L181L4
chr1:110256150-110256150p.N74N3
chr1:110257791-110257791p.M166V3
chr1:110257774-110257774p.A160V3
chr1:110257793-110257793p.M166I2
chr1:110256309-110256309p.R96C2
chr1:110255794-110255794p.D56Y2

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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
# sample1  5    1  35   62 3
# mutation1  4    1  35   62 3
nonsynonymous SNV1  4    1  33   52 1
synonymous SNV            2   1  2
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
chr1:110257755p.D56Y2
chr1:110255794p.D106N2
chr1:110256339p.E121E2
chr1:110257571p.T154A2
chr1:110254965p.R11C2
chr1:110255769p.L208L1
chr1:110257779p.E49K1
chr1:110255773p.D65Y1
chr1:110257798p.G66V1
chr1:110257831p.R96C1

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 GSTM5 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 GSTM5

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

AACS,ACSBG1,AKR1D1,LINC01554,CLEC4C,FCN2,GSTM2P1,
GSTM5,GSTT2,GUSB,HIST3H3,LOC91948,MAGEB3,MYOM2,
NANOG,LINC00160,NR1H4,RNASE11,RNASE12,SLC6A3,TMPRSS9
APOD,B4GALNT2,CCBL1,DHRS2,ENPP3,F9,GSTM2P1,
GSTM5,GUSB,HIST1H2AE,HIST1H2BG,HIST1H4H,HPD,NANOG,
NAT2,PPEF1,SPINK8,SPINT3,SULT1C3,TTC21A,UGT2B11

A2M,ABCA8,BOC,C7,COL14A1,DCLK1,FBLN1,
FBLN5,GSTM5,GYPC,LHFP,LIFR,MGP,PDE1A,
PLAC9,PNMAL2,PODN,RBMS3,SCN4B,SLIT3,TMEM130
AS3MT,CTSF,DCN,ZC2HC1A,FXYD1,GSTM5,LOC220930,
LOC284276,MEAF6,NDNL2,NME5,PLD5,PTN,RRAGB,
SNRPN,TIGD7,WASF3,ZNF470,ZNF542P,ZNF626,ZNF667
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 GSTM5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00143glutathione S-transferase mu 5approved; nutraceuticalGlutathione
DB00515glutathione S-transferase mu 5approvedCisplatin
DB01248glutathione S-transferase mu 5approved; investigationalDocetaxel


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Cross referenced IDs for GSTM5
* 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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