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 TPMT
Basic gene info.Gene symbolTPMT
Gene namethiopurine S-methyltransferase
Synonyms-
CytomapUCSC genome browser: 6p22.3
Genomic locationchr6 :18128544-18155374
Type of geneprotein-coding
RefGenesNM_000367.3,
Ensembl idENSG00000137364
DescriptionS-adenosyl-L-methionine:thiopurine S-methyltransferase
Modification date20141222
dbXrefs MIM : 187680
HGNC : HGNC
Ensembl : ENSG00000137364
HPRD : 01760
Vega : OTTHUMG00000014317
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPMT
BioGPS: 7172
Gene Expression Atlas: ENSG00000137364
The Human Protein Atlas: ENSG00000137364
PathwayNCI Pathway Interaction Database: TPMT
KEGG: TPMT
REACTOME: TPMT
ConsensusPathDB
Pathway Commons: TPMT
MetabolismMetaCyc: TPMT
HUMANCyc: TPMT
RegulationEnsembl's Regulation: ENSG00000137364
miRBase: chr6 :18,128,544-18,155,374
TargetScan: NM_000367
cisRED: ENSG00000137364
ContextiHOP: TPMT
cancer metabolism search in PubMed: TPMT
UCL Cancer Institute: TPMT
Assigned class in ccmGDBC

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

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

Mutations for TPMT
* 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 TPMT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU608204TPMT1935061812994518130276PHACTR23486586144148681144148991

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=15)		Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr6:18139944-18139944p.S124Y2
chr6:18148082-18148082p.L69V2
chr6:18139929-18139929p.S129L1
chr6:18149253-18149253p.G36S1
chr6:18149254-18149254p.N35N1
chr6:18130978-18130978p.V220A1
chr6:18143837-18143837p.K119T1
chr6:18149270-18149270p.Q30R1
chr6:18130994-18130994p.R215C1
chr6:18143892-18143893p.T101fs*221

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 5       1    22 2
# mutation 1 5       1    22 2
nonsynonymous SNV   3       1    21 2
synonymous SNV 1 2             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
chr6:18139944p.S124Y2
chr6:18149254p.R226Q1
chr6:18149270p.G209S1
chr6:18130960p.R206R1
chr6:18149277p.K176N1
chr6:18132364p.L174L1
chr6:18132371p.L138I1
chr6:18134087p.K119T1
chr6:18134095p.F67F1
chr6:18139903p.N35N1

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 TPMT 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 TPMT

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

ACOT13,LINC00305,C6orf62,MCUR1,DEK,FAM8A1,HIST1H2BB,
JARID2,KDM1B,KIF13A,MRS2,NHLRC1,NUP153,RIT2,
RNF144B,SLC35B3,SSR1,TDP2,TPMT,ZNF184,ZNF271P		AAGAB,AGPAT5,ATP6V1G1,BUB3,RHNO1,VWA9,C3orf14,
CD9,CDS1,HAT1,HSBP1,LCA5L,LRRC42,MTHFD2,
POLB,PPA2,SRP54,SSX2IP,SVIP,TPMT,USP10

ASS1,BAK1,BCL10,GSKIP,CYSTM1,F2RL1,GPA33,
IFNGR1,KDM1B,LGALS3,LGR4,LRRC1,MALL,MOB3B,
PLS1,PPP1R11,RPS6KA1,SLC35A3,TMEM45B,TMEM54,TPMT		ABHD3,ARPC5,CYSTM1,ABRACL,CDC42SE2,CHMP2B,MICU2,
GHITM,HIGD1A,HN1,LRRC19,MYL12A,MYL12B,NAT1,
ORMDL2,PEX13,SLMO2,STX12,TPMT,UBE2A,VPS26A
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 TPMT
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
DB01250thiopurine S-methyltransferaseapprovedOlsalazine
DB01234thiopurine S-methyltransferaseapproved; investigationalDexamethasone
DB00650thiopurine S-methyltransferaseapprovedLeucovorin
DB01248thiopurine S-methyltransferaseapproved; investigationalDocetaxel
DB00640thiopurine S-methyltransferaseapproved; investigationalAdenosine
DB00134thiopurine S-methyltransferaseapproved; nutraceuticalL-Methionine
DB01327thiopurine S-methyltransferaseapprovedCefazolin
DB00544thiopurine S-methyltransferaseapprovedFluorouracil
DB00762thiopurine S-methyltransferaseapproved; investigationalIrinotecan
DB00987thiopurine S-methyltransferaseapproved; investigationalCytarabine
DB00694thiopurine S-methyltransferaseapprovedDaunorubicin
DB00773thiopurine S-methyltransferaseapprovedEtoposide
DB01033thiopurine S-methyltransferaseapprovedMercaptopurine
DB00563thiopurine S-methyltransferaseapprovedMethotrexate
DB00635thiopurine S-methyltransferaseapprovedPrednisone
DB00541thiopurine S-methyltransferaseapproved; investigationalVincristine
DB00352thiopurine S-methyltransferaseapprovedThioguanine
DB00993thiopurine S-methyltransferaseapprovedAzathioprine
DB01454thiopurine S-methyltransferaseillicit; experimental3,4-Methylenedioxymethamphetamine
DB00668thiopurine S-methyltransferaseapprovedEpinephrine
DB00795thiopurine S-methyltransferaseapprovedSulfasalazine
DB00515thiopurine S-methyltransferaseapprovedCisplatin


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Cross referenced IDs for TPMT
* 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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