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 GSTM4
Basic gene info.Gene symbolGSTM4
Gene nameglutathione S-transferase mu 4
SynonymsGSTM4-4|GTM4
CytomapUCSC genome browser: 1p13.3
Genomic locationchr1 :110198697-110204331
Type of geneprotein-coding
RefGenesNM_000850.4,
NM_147148.2,NR_024538.1,NM_147149.1,
Ensembl idENSG00000168765
DescriptionGST class-mu 4GST-Mu2GTS-Mu2S-(hydroxyalkyl)glutathione lyase M4glutathione S-alkyltransferase M4glutathione S-aralkyltransferase M4glutathione S-aryltransferase M4glutathione S-transferase M4glutathione S-transferase Mu 4
Modification date20141207
dbXrefs MIM : 138333
HGNC : HGNC
Ensembl : ENSG00000168765
HPRD : 00706
Vega : OTTHUMG00000011642
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSTM4
BioGPS: 2948
Gene Expression Atlas: ENSG00000168765
The Human Protein Atlas: ENSG00000168765
PathwayNCI Pathway Interaction Database: GSTM4
KEGG: GSTM4
REACTOME: GSTM4
ConsensusPathDB
Pathway Commons: GSTM4
MetabolismMetaCyc: GSTM4
HUMANCyc: GSTM4
RegulationEnsembl's Regulation: ENSG00000168765
miRBase: chr1 :110,198,697-110,204,331
TargetScan: NM_000850
cisRED: ENSG00000168765
ContextiHOP: GSTM4
cancer metabolism search in PubMed: GSTM4
UCL Cancer Institute: GSTM4
Assigned class in ccmGDBC

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Phenotypic Information for GSTM4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GSTM4
Familial Cancer Database: GSTM4
* 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: GSTM4
MedGen: GSTM4 (Human Medical Genetics with Condition)
ClinVar: GSTM4
PhenotypeMGI: GSTM4 (International Mouse Phenotyping Consortium)
PhenomicDB: GSTM4

Mutations for GSTM4
* 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 GSTM4 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=18)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr1:110201710-110201710p.K182R2
chr1:110203869-110203869p.N217S2
chr1:110201532-110201532p.?1
chr1:110199865-110199865p.L47L1
chr1:110201636-110201636p.D157E1
chr1:110201725-110201725p.R187H1
chr1:110199871-110199871p.E49D1
chr1:110201637-110201637p.F158I1
chr1:110203784-110203784p.?1
chr1:110199884-110199884p.G54S1

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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  3  2    231  23 3
# mutation1  3  2    231  13 3
nonsynonymous SNV   3  1    13   12 3
synonymous SNV1     1    1 1   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
chr1:110207637p.S191F2
chr1:110201509p.A16D,GSTM41
chr1:110201655p.E29K,GSTM41
chr1:110201661p.P39P,GSTM41
chr1:110199040p.L47L,GSTM41
chr1:110201676p.R82C,GSTM41
chr1:110199342p.R96C,GSTM41
chr1:110201681p.R145K,GSTM41
chr1:110199344p.L164I,GSTM41
chr1:110201701p.L166I,GSTM41

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 GSTM4 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 GSTM4

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

ACBD4,ALG14,CCDC24,CIRBP,DNAJC17,FAAH,GAMT,
GATSL3,GNPTG,GSTM1,GSTM2,GSTM2P1,GSTM3,GSTM4,
LAMTOR5,HYI,NINJ1,PFDN5,SIRT3,TNFSF12,TSTD1
ATP5G3,ATP5H,ATP5J,PRADC1,COPS7A,COX6B1,COX7B,
ECH1,FUNDC2,GSTM4,LOC150381,MRPL40,NDUFA3,NDUFA6,
NDUFA8,NDUFAB1,NDUFAF1,NDUFV2,PDHB,UQCR10,UQCR11

ACADS,ATP5B,TMEM253,C17orf78,CCL25,CDC20B,CYP2C9,
GOT1,GPD1,GSTM4,IDH2,IDH3A,MTTP,MYO1A,
PLCB3,PRR13,PSMA5,RBP2,SLC7A9,SOAT2,TEKT1
APOM,ADIRF,TMEM252,GBA3,GCNT4,GOLT1A,SLC52A1,
GSTM4,HEBP1,HOXC8,MEP1B,NAT8B,OTC,PCK2,
PTGR1,SLC6A4,SULT1E1,TM6SF2,AGMO,PRSS3P2,TTC36
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 GSTM4
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 4approved; nutraceuticalGlutathione
DB03003glutathione S-transferase mu 4experimentalGlutathione Sulfonic Acid
DB03032glutathione S-transferase mu 4experimentalS-Octylglutathione
DB03597glutathione S-transferase mu 4experimentalGamma-Glutamyl[S-(2-Iodobenzyl)Cysteinyl]Glycine
DB03706glutathione S-transferase mu 4experimental1-Hydroxy-2-S-Glutathionyl-3-Para-Nitrophenoxy-Propane
DB04132glutathione S-transferase mu 4experimentalS-Hexylglutathione
DB00515glutathione S-transferase mu 4approvedCisplatin


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Cross referenced IDs for GSTM4
* 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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