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 MGST1
Basic gene info.Gene symbolMGST1
Gene namemicrosomal glutathione S-transferase 1
SynonymsGST12|MGST|MGST-I
CytomapUCSC genome browser: 12p12.3-p12.1
Genomic locationchr12 :16506350-16517344
Type of geneprotein-coding
RefGenesNM_001260511.1,
NM_001260512.1,NM_001267598.1,NM_020300.4,NM_145764.2,
NM_145791.2,NM_145792.2,NR_048545.1,NR_048547.1,
Ensembl idENSG00000008394
Descriptionglutathione S-transferase 12microsomal GST-1microsomal GST-I
Modification date20141207
dbXrefs MIM : 138330
HGNC : HGNC
Ensembl : ENSG00000008394
HPRD : 00705
Vega : OTTHUMG00000168816
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGST1
BioGPS: 4257
Gene Expression Atlas: ENSG00000008394
The Human Protein Atlas: ENSG00000008394
PathwayNCI Pathway Interaction Database: MGST1
KEGG: MGST1
REACTOME: MGST1
ConsensusPathDB
Pathway Commons: MGST1
MetabolismMetaCyc: MGST1
HUMANCyc: MGST1
RegulationEnsembl's Regulation: ENSG00000008394
miRBase: chr12 :16,506,350-16,517,344
TargetScan: NM_001260511
cisRED: ENSG00000008394
ContextiHOP: MGST1
cancer metabolism search in PubMed: MGST1
UCL Cancer Institute: MGST1
Assigned class in ccmGDBC

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Phenotypic Information for MGST1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MGST1
Familial Cancer Database: MGST1
* 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: MGST1
MedGen: MGST1 (Human Medical Genetics with Condition)
ClinVar: MGST1
PhenotypeMGI: MGST1 (International Mouse Phenotyping Consortium)
PhenomicDB: MGST1

Mutations for MGST1
* 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 MGST1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM983802MGST116296121651705816517338MGST1290517121651673116516958
AI910757MGST11270121651707016517339CRYZ26336917517266275172876
DB298359MGST11110121651723716517343SRGAP2935781206634771206635257

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
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
chr12:16510603-16510603p.R64Q4
chr12:16516725-16516725p.?2
chr12:16516748-16516748p.E81*1
chr12:16507203-16507203p.Q6L1
chr12:16516792-16516792p.L95F1
chr12:16507276-16507276p.M30I1
chr12:16516801-16516801p.P98P1
chr12:16510566-16510566p.A52S1
chr12:16516815-16516815p.A103V1
chr12:16510579-16510579p.G56V1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   2  1    221  13 4
# mutation   2  1    221  13 3
nonsynonymous SNV   2  1    121  13 3
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
chr12:16510603p.R64Q,MGST13
chr12:16516815p.Q6L,MGST11
chr12:16507203p.M8T,MGST11
chr12:16516845p.M8I,MGST11
chr12:16507209p.A52S,MGST11
chr12:16516939p.G56V,MGST11
chr12:16507210p.D67G,MGST11
chr12:16516968p.R73H,MGST11
chr12:16510566p.L95F,MGST11
chr12:16510579p.P98P,MGST11

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 MGST1 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 MGST1

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

CMAS,DBI,DDX47,DERA,ERGIC2,G6PD,GGCT,
IDH1,KMO,LPCAT3,MAGOHB,MGST1,MPHOSPH6,NDUFA9,
PERP,PEX13,RAB1A,SRD5A1,SRD5A3,STRAP,TPI1
ACO1,ASPH,FAM213A,PQLC2L,CAV1,CAV2,HRASLS5,
ITGB1BP1,MGST1,MMD,PALM2-AKAP2,PGRMC2,PLIN1,PLOD2,
PRKAR2B,PYGL,RTN3,SORBS1,TK2,TSPAN3,VKORC1L1

ATP5C1,ATP5G3,ATP5J2,COX5A,DERA,ETFA,HADH,
HINT1,MGST1,MRPL51,NDUFA12,NDUFA9,NUP37,PHB2,
PHF5A,PPA2,TPI1,TWF1,UBE2N,UQCRQ,YARS2
ADH1C,ARFIP1,ARL6IP1,CAAP1,MICU2,LHFPL3,MGST1,
MIPEP,MRPS30,MTCH2,MYCBP,NUDT15,PDHX,PIGF,
RTN4IP1,SCO1,SLC30A9,STEAP1,TMED5,TMX1,UQCRFS1
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 MGST1
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 1approved; nutraceuticalGlutathione


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Cross referenced IDs for MGST1
* 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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