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 MGST2

Basic gene info.	Gene symbol	MGST2
	Gene name	microsomal glutathione S-transferase 2
	Synonyms	GST2\|MGST-II
	Cytomap	UCSC genome browser: 4q28.3
	Genomic location	chr4 :140586921-140625406
	Type of gene	protein-coding
	RefGenes	NM_001204366.1, NM_001204367.1,NM_001204368.1,NM_002413.4,
	Ensembl id	ENSG00000085871
	Description	microsomal GST-2microsomal GST-II
	Modification date	20141207
dbXrefs	MIM : 601733
	HGNC : HGNC
	Ensembl : ENSG00000085871
	HPRD : 03436
	Vega : OTTHUMG00000133382
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGST2
	BioGPS: 4258
	Gene Expression Atlas: ENSG00000085871
	The Human Protein Atlas: ENSG00000085871
Pathway	NCI Pathway Interaction Database: MGST2
	KEGG: MGST2
	REACTOME: MGST2
	ConsensusPathDB
	Pathway Commons: MGST2
Metabolism	MetaCyc: MGST2
	HUMANCyc: MGST2
Regulation	Ensembl's Regulation: ENSG00000085871
	miRBase: chr4 :140,586,921-140,625,406
	TargetScan: NM_001204366
	cisRED: ENSG00000085871
Context	iHOP: MGST2
	cancer metabolism search in PubMed: MGST2
	UCL Cancer Institute: MGST2
Assigned class in ccmGDB	C

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Phenotypic Information for MGST2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MGST2
	Familial Cancer Database: MGST2

* 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: MGST2
	MedGen: MGST2 (Human Medical Genetics with Condition)
	ClinVar: MGST2
Phenotype	MGI: MGST2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MGST2

Mutations for MGST2

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	MGST2	chr4	140594739	140594759		chr4	141693269	141693289

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MGST2 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
BG208010	MGST2	1	56	4	140661367	140661422	PRDX6	53	255	1	173450488	173454567
AB058719	CYFIP2	1	175	5	156811175	156811349	MGST2	176	5164	4	140639642	141075233

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=5)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr4:140624683-140624683	p.K103fs*8	2
chr4:140625270-140625270	p.N138D	2
chr4:140599715-140599715	p.V26A	1
chr4:140599789-140599789	p.R51W	1
chr4:140616352-140616352	p.Q54*	1
chr4:140616381-140616381	p.F63F	1
chr4:140616421-140616421	p.V77I	1
chr4:140624670-140624670	p.Y97*	1
chr4:140625218-140625218	p.L120L	1
chr4:140625252-140625252	p.D132N	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=1

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										1			3	1
# mutation				1										1			3	1
nonsynonymous SNV				1										1			2	1
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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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
chr4:140625270	p.N70D,MGST2	2
chr4:140599715	p.V26A,MGST2	1
chr4:140616381	p.F63F,MGST2	1
chr4:140625225	p.A55T,MGST2	1
chr4:140625252	p.D64N,MGST2	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 MGST2 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 MGST2

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


ABHD14A,ATP5G2,C12orf10,EMC7,COA3,COX6A1,COX7C, MGST2,MRPL40,NDUFA2,NDUFB1,NDUFC1,NDUFV2,PARK7, PFDN5,RPL36AL,SERF2,SPR,SRP14,SYNC,WIBG	ATP6V0E1,CCDC53,DAD1,DYNLRB1,GABARAPL2,GNG5,GTF2A2, MGST2,NOP10,OST4,POLE4,POMP,PSMA3,RBX1, RHEB,RRAGA,SRP14,THOC7,TMEM14C,TOMM5,ZBTB8OS

ATP5G1,ATP5I,ATPIF1,TMEM258,TMA7,COPZ1,COX7A2, COX7C,FAM96B,LAMTOR5,HINT1,LSM6,MGST2,MRPS18C, MRPS36,NDUFA2,NDUFA7,NDUFC1,PRELID1,UQCRQ,USMG5	ATPIF1,MPC2,CASP6,CCL15,CENPV,GLOD4,HOXB7, JAGN1,MGST2,MRPS36,NDUFC1,NDUFC2,S100A14,SPCS1, SS18L2,SUCLG1,TMEM106C,UBAC2,UQCRQ,VPS25,ZBTB8OS

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 MGST2

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	microsomal glutathione S-transferase 2	approved; nutraceutical	Glutathione
DB01008	microsomal glutathione S-transferase 2	approved; investigational	Busulfan
DB01042	microsomal glutathione S-transferase 2	approved	Melphalan

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Cross referenced IDs for MGST2

* 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