Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	GSTM2
	Gene name	glutathione S-transferase mu 2 (muscle)
	Synonyms	GST4\|GSTM\|GSTM2-2\|GTHMUS
	Cytomap	UCSC genome browser: 1p13.3
	Genomic location	chr1 :110210643-110226619
	Type of gene	protein-coding
	RefGenes	NM_000848.3, NM_001142368.1,
	Ensembl id	ENSG00000213366
	Description	GST 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 date	20141207
dbXrefs	MIM : 138380
	HGNC : HGNC
	Ensembl : ENSG00000213366
	HPRD : 00710
	Vega : OTTHUMG00000011638
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTM2
	BioGPS: 2946
	Gene Expression Atlas: ENSG00000213366
	The Human Protein Atlas: ENSG00000213366
Pathway	NCI Pathway Interaction Database: GSTM2
	KEGG: GSTM2
	REACTOME: GSTM2
	ConsensusPathDB
	Pathway Commons: GSTM2
Metabolism	MetaCyc: GSTM2
	HUMANCyc: GSTM2
Regulation	Ensembl's Regulation: ENSG00000213366
	miRBase: chr1 :110,210,643-110,226,619
	TargetScan: NM_000848
	cisRED: ENSG00000213366
Context	iHOP: GSTM2
	cancer metabolism search in PubMed: GSTM2
	UCL Cancer Institute: GSTM2
Assigned class in ccmGDB	C

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Phenotypic Information for GSTM2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_GLUTATHIONE_METABOLISM KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450

Others
OMIM
Orphanet
Disease	KEGG Disease: GSTM2
	MedGen: GSTM2 (Human Medical Genetics with Condition)
	ClinVar: GSTM2
Phenotype	MGI: GSTM2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GSTM2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AW386100	GSTM2	1	446	1	110213886	110256544	EVC2	433	452	4	5671338	5671357
BU855095	GSTM2	1	579	1	110211922	110217567	RAN	579	870	12	131359137	131360301
BU859345	GSTM2	1	579	1	110211922	110217567	RAN	579	878	12	131359137	131360314
BI006168	EPB41L1	1	140	20	34819363	34819503	GSTM2	134	283	1	110210975	110211122
BG993988	PTRF	1	125	17	40554559	40554682	GSTM2	119	360	1	110214162	110217566
EB387269	ALG13	7	399	X	110935031	110935423	GSTM2	391	414	1	110220770	110220793

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr1:110212119-110212119	p.R96C	2
chr1:110217413-110217413	p.L204L	2
chr1:110211966-110211966	p.R78W	2
chr1:110211085-110211085	p.D25E	1
chr1:110211979-110211979	p.R82H	1
chr1:110217403-110217403	p.S201I	1
chr1:110211089-110211089	p.S27C	1
chr1:110211094-110211094	p.Y28Y	1
chr1:110212149-110212149	p.D106N	1
chr1:110217428-110217428	p.F209F	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2			3			1		1			2				1	2	2		2
# mutation	2			3			1		1			2				2	3	2		2
nonsynonymous SNV	1			3			1					2				1	2	1		2
synonymous SNV	1								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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:110217413	p.L204L	2
chr1:110211085	p.S201I	1
chr1:110213993	p.D25E,GSTM2	1
chr1:110211094	p.F209F	1
chr1:110214125	p.Y28Y,GSTM2	1
chr1:110211103	p.K31N,GSTM2	1
chr1:110214126	p.L47L,GSTM2	1
chr1:110211575	p.T67A,GSTM2	1
chr1:110217403	p.R82H,GSTM2	1
chr1:110211933	p.R96C,GSTM2	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00143	glutathione S-transferase mu 2 (muscle)	approved; nutraceutical	Glutathione
DB02458	glutathione S-transferase mu 2 (muscle)	experimental	Glutathione S-(2,4 Dinitrobenzene)
DB03310	glutathione S-transferase mu 2 (muscle)	experimental	Oxidized Glutathione Disulfide
DB04701	glutathione S-transferase mu 2 (muscle)	experimental	S-METHYL-GLUTATHIONE
DB00515	glutathione S-transferase mu 2 (muscle)	approved	Cisplatin
DB01008	glutathione S-transferase mu 2 (muscle)	approved; investigational	Busulfan
DB00988	glutathione S-transferase mu 2 (muscle)	approved	Dopamine
DB00668	glutathione S-transferase mu 2 (muscle)	approved	Epinephrine

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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