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 MGST2
Basic gene info.Gene symbolMGST2
Gene namemicrosomal glutathione S-transferase 2
SynonymsGST2|MGST-II
CytomapUCSC genome browser: 4q28.3
Genomic locationchr4 :140586921-140625406
Type of geneprotein-coding
RefGenesNM_001204366.1,
NM_001204367.1,NM_001204368.1,NM_002413.4,
Ensembl idENSG00000085871
Descriptionmicrosomal GST-2microsomal GST-II
Modification date20141207
dbXrefs MIM : 601733
HGNC : HGNC
Ensembl : ENSG00000085871
HPRD : 03436
Vega : OTTHUMG00000133382
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGST2
BioGPS: 4258
Gene Expression Atlas: ENSG00000085871
The Human Protein Atlas: ENSG00000085871
PathwayNCI Pathway Interaction Database: MGST2
KEGG: MGST2
REACTOME: MGST2
ConsensusPathDB
Pathway Commons: MGST2
MetabolismMetaCyc: MGST2
HUMANCyc: MGST2
RegulationEnsembl's Regulation: ENSG00000085871
miRBase: chr4 :140,586,921-140,625,406
TargetScan: NM_001204366
cisRED: ENSG00000085871
ContextiHOP: MGST2
cancer metabolism search in PubMed: MGST2
UCL Cancer Institute: MGST2
Assigned class in ccmGDBC

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Phenotypic Information for MGST2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

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: MGST2
MedGen: MGST2 (Human Medical Genetics with Condition)
ClinVar: MGST2
PhenotypeMGI: MGST2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryMGST2chr4140594739140594759chr4141693269141693289
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MGST2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG208010MGST21564140661367140661422PRDX6532551173450488173454567
AB058719CYFIP211755156811175156811349MGST217651644140639642141075233

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=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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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
chr4:140624683-140624683p.K103fs*82
chr4:140625270-140625270p.N138D2
chr4:140624670-140624670p.Y97*1
chr4:140625218-140625218p.L120L1
chr4:140625252-140625252p.D132N1
chr4:140599715-140599715p.V26A1
chr4:140599789-140599789p.R51W1
chr4:140616352-140616352p.Q54*1
chr4:140616381-140616381p.F63F1
chr4:140616421-140616421p.V77I1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1         1  31  
# mutation   1         1  31  
nonsynonymous SNV   1         1  21  
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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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
chr4:140625270p.N70D,MGST22
chr4:140599715p.V26A,MGST21
chr4:140616381p.F63F,MGST21
chr4:140625225p.A55T,MGST21
chr4:140625252p.D64N,MGST21

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 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

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

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
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 MGST2
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
DB00143microsomal glutathione S-transferase 2approved; nutraceuticalGlutathione
DB01008microsomal glutathione S-transferase 2approved; investigationalBusulfan
DB01042microsomal glutathione S-transferase 2approvedMelphalan


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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



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