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 GSTM2
Basic gene info.Gene symbolGSTM2
Gene nameglutathione S-transferase mu 2 (muscle)
SynonymsGST4|GSTM|GSTM2-2|GTHMUS
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :110210643-110226619
Type of geneprotein-coding
RefGenesNM_000848.3,
NM_001142368.1,
Ensembl idENSG00000213366
DescriptionGST class-mu 2GST, muscleS-(hydroxyalkyl)glutathione lyase M2glutathione S-alkyltransferase M2glutathione S-aralkyltransferase M2glutathione S-aryltransferase M2glutathione S-transferase 4glutathione S-transferase M1glutathione S-transferase M2 (m
Modification date20141207
dbXrefs MIM : 138380
HGNC : HGNC
Ensembl : ENSG00000213366
HPRD : 00710
Vega : OTTHUMG00000011638
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSTM2
BioGPS: 2946
Gene Expression Atlas: ENSG00000213366
The Human Protein Atlas: ENSG00000213366
PathwayNCI Pathway Interaction Database: GSTM2
KEGG: GSTM2
REACTOME: GSTM2
ConsensusPathDB
Pathway Commons: GSTM2
MetabolismMetaCyc: GSTM2
HUMANCyc: GSTM2
RegulationEnsembl's Regulation: ENSG00000213366
miRBase: chr1 :110,210,643-110,226,619
TargetScan: NM_000848
cisRED: ENSG00000213366
ContextiHOP: GSTM2
cancer metabolism search in PubMed: GSTM2
UCL Cancer Institute: GSTM2
Assigned class in ccmGDBC

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Phenotypic Information for GSTM2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GSTM2
Familial Cancer Database: GSTM2
* 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: GSTM2
MedGen: GSTM2 (Human Medical Genetics with Condition)
ClinVar: GSTM2
PhenotypeMGI: GSTM2 (International Mouse Phenotyping Consortium)
PhenomicDB: GSTM2

Mutations for GSTM2
* 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 GSTM2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW386100GSTM214461110213886110256544EVC2433452456713385671357
BU855095GSTM215791110211922110217567RAN57987012131359137131360301
BU859345GSTM215791110211922110217567RAN57987812131359137131360314
BI006168EPB41L11140203481936334819503GSTM21342831110210975110211122
BG993988PTRF1125174055455940554682GSTM21193601110214162110217566
EB387269ALG137399X110935031110935423GSTM23914141110220770110220793

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 # sample                1
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)

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr1:110211966-110211966p.R78W2
chr1:110212119-110212119p.R96C2
chr1:110217413-110217413p.L204L2
chr1:110211613-110211613p.?1
chr1:110213993-110213993p.L149I1
chr1:110211960-110211960p.I76V1
chr1:110214125-110214125p.V163I1
chr1:110214126-110214126p.V163A1
chr1:110211085-110211085p.D25E1
chr1:110211979-110211979p.R82H1

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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
# sample2  3  1 1  2   122 2
# mutation2  3  1 1  2   232 2
nonsynonymous SNV1  3  1    2   121 2
synonymous SNV1       1      111  
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
chr1:110217413p.L204L2
chr1:110212186p.V163A,GSTM21
chr1:110213924p.S201I1
chr1:110213937p.D25E,GSTM21
chr1:110211085p.F209F1
chr1:110213993p.Y28Y,GSTM21
chr1:110211094p.K31N,GSTM21
chr1:110214125p.L47L,GSTM21
chr1:110211103p.T67A,GSTM21
chr1:110214126p.R82H,GSTM21

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 GSTM2 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 GSTM2

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

ACAA1,APOD,CLPSL2,CCBL1,CCDC152,CCDC57,CHRNA10,
DCXR,DHRS4,DHRS4L2,ECHDC2,GAMT,GSTM1,GSTM2,
GSTM2P1,GSTM3,GSTM4,MYPN,REEP6,TP53TG1,TTC36
ADAM2,APOD,DHRS2,ENPP3,FDFT1,GSTM1,GSTM2,
HAAO,HIST1H4H,NANOG,NAT2,PLA2G4E,PNLIPRP3,PPEF1,
SERHL2,SERHL,SLC15A1,SNAP91,SPINK8,SULT1C3,UGT2B11

ADHFE1,ANKRD53,BHMT2,MILR1,CC2D2B,CORO6,CXCL12,
EVL,GRM5,GSTM1,GSTM2,GSTM5,HVCN1,IL18BP,
KLHDC7B,KRT1,LOC144571,NRROS,MBL1P,PCDH9,VEGFC
AGPAT4,AGTR2,PIANP,SERTM1,C1orf194,CLVS1,FOXF1,
GSTM1,GSTM2,KCNQ2,LOC339047,MAGED4B,MAPT,PLA2G2C,
RYR2,SHC2,SOX11,TMEM178A,TRIP6,UNC80,ZNF578
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 GSTM2
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 2 (muscle)approved; nutraceuticalGlutathione
DB02458glutathione S-transferase mu 2 (muscle)experimentalGlutathione S-(2,4 Dinitrobenzene)
DB03310glutathione S-transferase mu 2 (muscle)experimentalOxidized Glutathione Disulfide
DB04701glutathione S-transferase mu 2 (muscle)experimentalS-METHYL-GLUTATHIONE
DB00515glutathione S-transferase mu 2 (muscle)approvedCisplatin
DB01008glutathione S-transferase mu 2 (muscle)approved; investigationalBusulfan
DB00988glutathione S-transferase mu 2 (muscle)approvedDopamine
DB00668glutathione S-transferase mu 2 (muscle)approvedEpinephrine


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Cross referenced IDs for GSTM2
* 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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