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 MPST
Basic gene info.Gene symbolMPST
Gene namemercaptopyruvate sulfurtransferase
SynonymsMST|TST2|TUM1
CytomapUCSC genome browser: 22q13.1
Genomic locationchr22 :37415682-37425863
Type of geneprotein-coding
RefGenesNM_001013436.2,
NM_001130517.2,NM_021126.5,NM_001013440.1,NR_024038.1,
Ensembl idENSG00000128309
Description3-mercaptopyruvate sulfurtransferasehuman liver rhodanesetRNA thiouridin modification protein 1
Modification date20141215
dbXrefs MIM : 602496
HGNC : HGNC
Ensembl : ENSG00000128309
HPRD : 11896
Vega : OTTHUMG00000150543
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MPST
BioGPS: 4357
Gene Expression Atlas: ENSG00000128309
The Human Protein Atlas: ENSG00000128309
PathwayNCI Pathway Interaction Database: MPST
KEGG: MPST
REACTOME: MPST
ConsensusPathDB
Pathway Commons: MPST
MetabolismMetaCyc: MPST
HUMANCyc: MPST
RegulationEnsembl's Regulation: ENSG00000128309
miRBase: chr22 :37,415,682-37,425,863
TargetScan: NM_001013436
cisRED: ENSG00000128309
ContextiHOP: MPST
cancer metabolism search in PubMed: MPST
UCL Cancer Institute: MPST
Assigned class in ccmGDBC

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Phenotypic Information for MPST(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MPST
Familial Cancer Database: MPST
* 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_CYSTEINE_AND_METHIONINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MPST
MedGen: MPST (Human Medical Genetics with Condition)
ClinVar: MPST
PhenotypeMGI: MPST (International Mouse Phenotyping Consortium)
PhenomicDB: MPST

Mutations for MPST
* 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 MPST related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF516432VAT11881174116662441166687MPST81152223742573637425807
CB164510MPST1217223742562337425839WAS211557X4854779248549812
CB157649MPST6240223742562337425856WAS234457X4854779248549689

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr22:37425453-37425453p.C264C1
chr22:37420465-37420465p.S70*1
chr22:37420784-37420785p.R177fs*251
chr22:37425508-37425508p.A283T1
chr22:37420502-37420502p.F82F1
chr22:37420785-37420785p.R177C1
chr22:37420583-37420583p.S109S1
chr22:37420797-37420797p.V181L1
chr22:37420588-37420588p.P111L1
chr22:37420806-37420806p.R184G1

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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  11   72 1
# mutation        1  11   72 1
nonsynonymous SNV        1  1    22  
synonymous SNV            1   5  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
chr22:37420676p.A261A,MPST1
chr22:37420687p.Y272Y,MPST1
chr22:37420785p.G56G,MPST1
chr22:37420797p.S109S,MPST1
chr22:37420806p.F117F,MPST1
chr22:37420837p.L140L,MPST1
chr22:37425309p.S144F,MPST1
chr22:37425350p.R177C,MPST1
chr22:37420424p.V181L,MPST1
chr22:37425399p.R184G,MPST1

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 MPST 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 MPST

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

AURKAIP1,CCDC124,DPM3,LSM7,MCAT,MIIP,MPST,
NDUFB11,NDUFB7,NOL12,PICK1,POLR2F,POLR2I,PQBP1,
PRR5,RBM42,RPS19BP1,SDHAF1,TRABD,TSPO,TST
BSG,C20orf27,DCXR,EIF4EBP1,ETFB,FPGS,GCDH,
MPST,PCYT2,PLEKHJ1,PMM1,POLR2E,PQLC1,PSMA7,
PXMP2,RPLP2,SLC25A10,SLC2A4RG,TALDO1,TMEM120A,TST

SMDT1,C4orf48,COMT,DDT,DDTL,EIF3D,HIGD2A,
MIF,MPST,NOL12,PICK1,POLR2F,PRR5,SLC25A1,
TMEM191A,TRAF4,TRMT2A,TST,TXN2,UQCR10,YDJC
ACADS,ACSF3,KDF1,CBLC,DCAF11,ELMO3,EPN1,
ESPN,ESRRA,GPR35,KLC4,MGAT4B,C8orf82,MPST,
PEX11G,PEX16,PPAP2C,PRKCZ,PRRG2,RILP,TMUB1
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 MPST
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
DB02761mercaptopyruvate sulfurtransferaseexperimentalS-Mercaptocysteine
DB03352mercaptopyruvate sulfurtransferaseexperimentalS-Arsonocysteine


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Cross referenced IDs for MPST
* 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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