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 GSTM3

Basic gene info.	Gene symbol	GSTM3
	Gene name	glutathione S-transferase mu 3 (brain)
	Synonyms	GST5\|GSTB\|GSTM3-3\|GTM3
	Cytomap	UCSC genome browser: 1p13.3
	Genomic location	chr1 :110276553-110283660
	Type of gene	protein-coding
	RefGenes	NM_000849.4, NR_024537.1,
	Ensembl id	ENSG00000134202
	Description	GST class-mu 3S-(hydroxyalkyl)glutathione lyase M3brain GSTbrain type mu-glutathione S-transferaseglutathione S-alkyltransferase M3glutathione S-aralkyltransferase M3glutathione S-aryltransferase M3glutathione S-transferase M3 (brain)glutathione S
	Modification date	20141207
dbXrefs	MIM : 138390
	HGNC : HGNC
	Ensembl : ENSG00000134202
	HPRD : 00712
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTM3
	BioGPS: 2947
	Gene Expression Atlas: ENSG00000134202
	The Human Protein Atlas: ENSG00000134202
Pathway	NCI Pathway Interaction Database: GSTM3
	KEGG: GSTM3
	REACTOME: GSTM3
	ConsensusPathDB
	Pathway Commons: GSTM3
Metabolism	MetaCyc: GSTM3
	HUMANCyc: GSTM3
Regulation	Ensembl's Regulation: ENSG00000134202
	miRBase: chr1 :110,276,553-110,283,660
	TargetScan: NM_000849
	cisRED: ENSG00000134202
Context	iHOP: GSTM3
	cancer metabolism search in PubMed: GSTM3
	UCL Cancer Institute: GSTM3
Assigned class in ccmGDB	C

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Phenotypic Information for GSTM3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GSTM3
	Familial Cancer Database: GSTM3

* 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: GSTM3
	MedGen: GSTM3 (Human Medical Genetics with Condition)
	ClinVar: GSTM3
Phenotype	MGI: GSTM3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GSTM3

Mutations for GSTM3

* 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 GSTM3 related fusion information.

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

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

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

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr1:110280786-110280786	p.R100Q	2
chr1:110279777-110279777	p.I198I	2
chr1:110280763-110280763	p.V108I	1
chr1:110282101-110282101	p.R47*	1
chr1:110280288-110280288	p.A153V	1
chr1:110280785-110280785	p.R100R	1
chr1:110282108-110282108	p.D44D	1
chr1:110280297-110280297	p.S150L	1
chr1:110282492-110282492	p.D29D	1
chr1:110280306-110280306	p.G147E	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		1		4							1	1	1		1		4	3	1	3
# mutation		1		5							1	1	1		1		4	3	1	3
nonsynonymous SNV				3							1	1	1		1		2	2	1	3
synonymous SNV		1		2													2	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
chr1:110282108	p.D110D	1
chr1:110280306	p.C91F	1
chr1:110282492	p.R86C	1
chr1:110280341	p.R82H	1
chr1:110282526	p.R82C	1
chr1:110280350	p.S204A	1
chr1:110279761	p.K73K	1
chr1:110280727	p.Q203K	1
chr1:110279764	p.D44D	1
chr1:110280755	p.A199T	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 GSTM3 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 GSTM3

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


ABCD3,ACBD4,ACOT4,C1orf64,CCDC103,CNTD1,CST9, EFHD1,GSTM2,GSTM3,GSTM4,KRT19,LOC100130581,MAGED2, ZNF205-AS1,PPT1,REEP5,RUNDC1,STC2,TMEM101,TTC39A	AAGAB,LINC00324,CAMK2N1,DNALI1,EFHD1,EIF2AK1,ERBB4, FOXA1,GLOD5,GSTM3,LYPD6B,MLPH,MYB,PPAPDC1B, PPT1,RFX6,SPA17,TMEM116,TSPAN13,TTC39A,XBP1

ASIC1,CACNG6,CCK,DGCR5,FBXO2,GSTM3,HGFAC, LRRC42,MRTO4,PAK7,PARK7,PEX10,PPCS,PPP1R2, SLIT1,SOHLH1,SPDYC,SSU72,TCHH,TEX19,ZNF735	ALDH1A1,ANO6,BEX1,BTC,LYRM9,C1QTNF3,C4orf3, CA11,CACNB2,DDHD2,ECM2,DENND6A,GSTM3,KRT222, CPQ,RGS5,SEC22C,STK33,TMEM64,XPA,ZNF639

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 GSTM3

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 3 (brain)	approved; nutraceutical	Glutathione
DB00958	glutathione S-transferase mu 3 (brain)	approved	Carboplatin
DB00997	glutathione S-transferase mu 3 (brain)	approved; investigational	Doxorubicin
DB01181	glutathione S-transferase mu 3 (brain)	approved	Ifosfamide
DB00515	glutathione S-transferase mu 3 (brain)	approved	Cisplatin
DB00531	glutathione S-transferase mu 3 (brain)	approved; investigational	Cyclophosphamide

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Cross referenced IDs for GSTM3

* 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