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 GSTM1
Basic gene info.Gene symbolGSTM1
Gene nameglutathione S-transferase mu 1
SynonymsGST1|GSTM1-1|GSTM1a-1a|GSTM1b-1b|GTH4|GTM1|H-B|MU|MU-1
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :110230417-110236367
Type of geneprotein-coding
RefGenesNM_000561.3,
NM_146421.2,
Ensembl idENSG00000134184
DescriptionGST HB subunit 4GST class-mu 1HB subunit 4S-(hydroxyalkyl)glutathione lyaseglutathione S-alkyltransferaseglutathione S-aralkyltransferaseglutathione S-aryltransferaseglutathione S-transferase M1glutathione S-transferase Mu 1
Modification date20141222
dbXrefs MIM : 138350
HGNC : HGNC
Ensembl : ENSG00000134184
HPRD : 00707
Vega : OTTHUMG00000011635
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSTM1
BioGPS: 2944
Gene Expression Atlas: ENSG00000134184
The Human Protein Atlas: ENSG00000134184
PathwayNCI Pathway Interaction Database: GSTM1
KEGG: GSTM1
REACTOME: GSTM1
ConsensusPathDB
Pathway Commons: GSTM1
MetabolismMetaCyc: GSTM1
HUMANCyc: GSTM1
RegulationEnsembl's Regulation: ENSG00000134184
miRBase: chr1 :110,230,417-110,236,367
TargetScan: NM_000561
cisRED: ENSG00000134184
ContextiHOP: GSTM1
cancer metabolism search in PubMed: GSTM1
UCL Cancer Institute: GSTM1
Assigned class in ccmGDBC

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Phenotypic Information for GSTM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GSTM1
Familial Cancer Database: GSTM1
* 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: GSTM1
MedGen: GSTM1 (Human Medical Genetics with Condition)
ClinVar: GSTM1
PhenotypeMGI: GSTM1 (International Mouse Phenotyping Consortium)
PhenomicDB: GSTM1

Mutations for GSTM1
* 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 GSTM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE091541EIF4EBP24290107218272872183014GSTM12876531110232905110236002

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=16)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr1:110233147-110233147p.D176D3
chr1:110233138-110233138p.K173N2
chr1:110231873-110231873p.R96C1
chr1:110233128-110233128p.F170C1
chr1:110231874-110231874p.R96L1
chr1:110231875-110231875p.R96R1
chr1:110230504-110230504p.M3I1
chr1:110232900-110232900p.L123R1
chr1:110233169-110233169p.F184V1
chr1:110230795-110230795p.A14P1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   2    21 1    21 2
# mutation   2    21 1    21 2
nonsynonymous SNV   1    21 1    21 2
synonymous SNV   1                
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
chr1:110233138p.M3I,GSTM11
chr1:110233169p.S27N,GSTM11
chr1:110235905p.E30K,GSTM11
chr1:110230504p.E30D,GSTM11
chr1:110230835p.R82C,GSTM11
chr1:110230843p.R96C,GSTM11
chr1:110230845p.R96R,GSTM11
chr1:110231736p.L123R,GSTM11
chr1:110231873p.K173N1
chr1:110231875p.F184V1

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 GSTM1 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 GSTM1

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

ABCG2,APOD,BAGE,CASP14,CCDC152,CHRNA10,EGLN3,
ENTHD1,GSTM1,GSTM2,GSTM2P1,GSTM3,GSTM4,KCNK12,
LOC731779,MCHR1,MYPN,SEPP1,SLC10A1,TRIM54,ZNF613
ADAM2,APOD,CPB2,DHRS2,ENPP3,GSTM1,GSTM2,
HAAO,HIST1H4H,ISX,NANOG,NAT2,PLA2G4E,PNLIPRP3,
PPEF1,SERHL2,SERHL,SLC15A1,SNAP91,SULT1C3,UGT2B11

C11orf85,ANKUB1,DPY19L2P4,GRM5,GSTM1,GSTM2,GUCA1C,
HLA-DQB1,IL1RL1,KHDC1L,KLHDC7B,KRT1,KRT81,OR10H4,
OR13H1,PCDH9,PLGLA,PRSS21,SPANXA2,SPANXB2,UTS2B
LURAP1L,CDH4,CEP170P1,DPYSL4,GSTM1,GSTM2,H3F3B,
HMGN3,LEPREL1,LOC285780,LOC441455,LSM12,MIP,NCOA7,
OR52I1,PEX5L,PPIC,PSG9,SNRNP35,UPK2,DAW1
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 GSTM1
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 1approved; nutraceuticalGlutathione
DB01834glutathione S-transferase mu 1experimental(9r,10r)-9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
DB02165glutathione S-transferase mu 1experimentalZinc Trihydroxide
DB02458glutathione S-transferase mu 1experimentalGlutathione S-(2,4 Dinitrobenzene)
DB03314glutathione S-transferase mu 1experimentalFluorotryptophane
DB04187glutathione S-transferase mu 1experimental(9s,10s)-9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
DB01234glutathione S-transferase mu 1approved; investigationalDexamethasone
DB04572glutathione S-transferase mu 1approvedThiotepa
DB01248glutathione S-transferase mu 1approved; investigationalDocetaxel
DB00412glutathione S-transferase mu 1approved; investigationalRosiglitazone
DB00993glutathione S-transferase mu 1approvedAzathioprine
DB01181glutathione S-transferase mu 1approvedIfosfamide
DB00526glutathione S-transferase mu 1approved; investigationalOxaliplatin
DB00445glutathione S-transferase mu 1approvedEpirubicin
DB00951glutathione S-transferase mu 1approvedIsoniazid
DB00515glutathione S-transferase mu 1approvedCisplatin
DB00531glutathione S-transferase mu 1approved; investigationalCyclophosphamide
DB00544glutathione S-transferase mu 1approvedFluorouracil
DB00291glutathione S-transferase mu 1approvedChlorambucil
DB00997glutathione S-transferase mu 1approved; investigationalDoxorubicin
DB01204glutathione S-transferase mu 1approved; investigationalMitoxantrone
DB00444glutathione S-transferase mu 1approvedTeniposide
DB01008glutathione S-transferase mu 1approved; investigationalBusulfan
DB01042glutathione S-transferase mu 1approvedMelphalan
DB00564glutathione S-transferase mu 1approved; investigationalCarbamazepine
DB00987glutathione S-transferase mu 1approved; investigationalCytarabine
DB00694glutathione S-transferase mu 1approvedDaunorubicin
DB00773glutathione S-transferase mu 1approvedEtoposide
DB00650glutathione S-transferase mu 1approvedLeucovorin
DB01033glutathione S-transferase mu 1approvedMercaptopurine
DB00563glutathione S-transferase mu 1approvedMethotrexate
DB00635glutathione S-transferase mu 1approvedPrednisone
DB00541glutathione S-transferase mu 1approved; investigationalVincristine
DB01143glutathione S-transferase mu 1approved; investigationalAmifostine
DB00958glutathione S-transferase mu 1approvedCarboplatin
DB01229glutathione S-transferase mu 1approvedPaclitaxel
DB01101glutathione S-transferase mu 1approved; investigationalCapecitabine
DB00762glutathione S-transferase mu 1approved; investigationalIrinotecan
DB00382glutathione S-transferase mu 1approvedTacrine
DB01060glutathione S-transferase mu 1approvedAmoxicillin
DB00766glutathione S-transferase mu 1approvedClavulanate
DB00197glutathione S-transferase mu 1withdrawnTroglitazone


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Cross referenced IDs for GSTM1
* 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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