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 MGST3

Basic gene info.	Gene symbol	MGST3
	Gene name	microsomal glutathione S-transferase 3
	Synonyms	GST-III
	Cytomap	UCSC genome browser: 1q23
	Genomic location	chr1 :165600109-165625372
	Type of gene	protein-coding
	RefGenes	NM_004528.3,
	Ensembl id	ENSG00000143198
	Description	microsomal GST-3microsomal GST-IIImicrosomal glutathione S-transferase III
	Modification date	20141207
dbXrefs	MIM : 604564
	HGNC : HGNC
	Ensembl : ENSG00000143198
	HPRD : 05192
	Vega : OTTHUMG00000034627
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGST3
	BioGPS: 4259
	Gene Expression Atlas: ENSG00000143198
	The Human Protein Atlas: ENSG00000143198
Pathway	NCI Pathway Interaction Database: MGST3
	KEGG: MGST3
	REACTOME: MGST3
	ConsensusPathDB
	Pathway Commons: MGST3
Metabolism	MetaCyc: MGST3
	HUMANCyc: MGST3
Regulation	Ensembl's Regulation: ENSG00000143198
	miRBase: chr1 :165,600,109-165,625,372
	TargetScan: NM_004528
	cisRED: ENSG00000143198
Context	iHOP: MGST3
	cancer metabolism search in PubMed: MGST3
	UCL Cancer Institute: MGST3
Assigned class in ccmGDB	C

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Phenotypic Information for MGST3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MGST3
	Familial Cancer Database: MGST3

* 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: MGST3
	MedGen: MGST3 (Human Medical Genetics with Condition)
	ClinVar: MGST3
Phenotype	MGI: MGST3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MGST3

Mutations for MGST3

* 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 MGST3 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
BG956101	MGST3	8	239	1	165623821	165624056	TRAPPC6A	227	420	19	45666435	45667474
DW407758	MGST3	18	304	1	165600465	165621237	SPOP	305	473	17	47677802	47679312

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=10)	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
chr1:165624721-165624721	p.G147R	2
chr1:165624622-165624622	p.R114*	2
chr1:165624701-165624701	p.V140A	2
chr1:165619127-165619127	p.G15S	1
chr1:165619140-165619140	p.F19S	1
chr1:165620301-165620301	p.C56*	1
chr1:165623542-165623542	p.A92A	1
chr1:165623555-165623555	p.R97*	1
chr1:165623566-165623566	p.Y100Y	1
chr1:165624643-165624643	p.A121T	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												2					2			3
# mutation												4					2			3
nonsynonymous SNV												3					1			2
synonymous SNV												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
chr1:165619154	p.T46T	1
chr1:165620271	p.P83Q	1
chr1:165621271	p.I85L	1
chr1:165623519	p.A92A	1
chr1:165623542	p.A121T	1
chr1:165624643	p.L122L	1
chr1:165624648	p.A2T	1
chr1:165619088	p.F19S	1
chr1:165619140	p.H24N	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 MGST3 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 MGST3

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


ACBD6,DUSP23,GBAP1,HAX1,JTB,KRTCAP2,MGST3, MRPL24,MRPL55,MTX1,NENF,PRCC,PRDX6,PSMB4, PSMD4,LAMTOR2,S100A11,SCAMP3,SCNM1,SNRPE,SSR2	ACAA2,ACOT6,MROH8,CYSTM1,CD99L2,EIF2B3,HSDL2, IAH1,MGST3,MSRB2,NFU1,NKAPL,POLR3GL,PPP1R1A, RTN4,SNAPIN,TSPAN3,TTC7B,UGP2,VEGFB,YWHAG

APH1A,ARF1,ARPC5,ARV1,BPNT1,CYSTM1,ETHE1, GIPC1,JTB,MGST3,MRPL24,MRPS14,RAB25,RABIF, LAMTOR2,S100A10,S100A11,S100A6,SDHC,TAGLN2,TPM3	BPNT1,ABRACL,COX6A1,CRYL1,ETFA,LGALS3,MAD2L1BP, MGST3,MLX,MYL12B,NAT2,NCOA4,SLC51B,SDHB, SLC25A20,SLC25A5,SLMO2,TACO1,TP53TG1,UQCRQ,WIBG

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 MGST3

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 3	approved; nutraceutical	Glutathione

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Cross referenced IDs for MGST3

* 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