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 MGST3
Basic gene info.Gene symbolMGST3
Gene namemicrosomal glutathione S-transferase 3
SynonymsGST-III
CytomapUCSC genome browser: 1q23
Genomic locationchr1 :165600109-165625372
Type of geneprotein-coding
RefGenesNM_004528.3,
Ensembl idENSG00000143198
Descriptionmicrosomal GST-3microsomal GST-IIImicrosomal glutathione S-transferase III
Modification date20141207
dbXrefs MIM : 604564
HGNC : HGNC
Ensembl : ENSG00000143198
HPRD : 05192
Vega : OTTHUMG00000034627
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGST3
BioGPS: 4259
Gene Expression Atlas: ENSG00000143198
The Human Protein Atlas: ENSG00000143198
PathwayNCI Pathway Interaction Database: MGST3
KEGG: MGST3
REACTOME: MGST3
ConsensusPathDB
Pathway Commons: MGST3
MetabolismMetaCyc: MGST3
HUMANCyc: MGST3
RegulationEnsembl's Regulation: ENSG00000143198
miRBase: chr1 :165,600,109-165,625,372
TargetScan: NM_004528
cisRED: ENSG00000143198
ContextiHOP: MGST3
cancer metabolism search in PubMed: MGST3
UCL Cancer Institute: MGST3
Assigned class in ccmGDBC

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Phenotypic Information for MGST3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

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: MGST3
MedGen: MGST3 (Human Medical Genetics with Condition)
ClinVar: MGST3
PhenotypeMGI: MGST3 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MGST3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG956101MGST382391165623821165624056TRAPPC6A227420194566643545667474
DW407758MGST3183041165600465165621237SPOP305473174767780247679312

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2                
GAIN (# sample)2                
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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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=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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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
chr1:165624701-165624701p.V140A2
chr1:165624721-165624721p.G147R2
chr1:165624622-165624622p.R114*2
chr1:165624648-165624648p.L122L1
chr1:165619088-165619088p.A2T1
chr1:165619116-165619116p.V11E1
chr1:165619127-165619127p.G15S1
chr1:165619140-165619140p.F19S1
chr1:165620301-165620301p.C56*1
chr1:165623542-165623542p.A92A1

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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           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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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
chr1:165619088p.A2T1
chr1:165619140p.F19S1
chr1:165619154p.H24N1
chr1:165620271p.T46T1
chr1:165621271p.P83Q1
chr1:165623519p.I85L1
chr1:165623542p.A92A1
chr1:165624643p.A121T1
chr1:165624648p.L122L1

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 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

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

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
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 MGST3
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 3approved; nutraceuticalGlutathione


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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



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