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 TYMS
Basic gene info.Gene symbolTYMS
Gene namethymidylate synthetase
SynonymsHST422|TMS|TS
CytomapUCSC genome browser: 18p11.32
Genomic locationchr18 :657603-673499
Type of geneprotein-coding
RefGenesNM_001071.2,
Ensembl idENSG00000176890
DescriptionTSasethymidylate synthase
Modification date20141207
dbXrefs MIM : 188350
HGNC : HGNC
Ensembl : ENSG00000176890
HPRD : 01774
Vega : OTTHUMG00000131473
ProteinUniProt: P04818
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TYMS
BioGPS: 7298
Gene Expression Atlas: ENSG00000176890
The Human Protein Atlas: ENSG00000176890
PathwayNCI Pathway Interaction Database: TYMS
KEGG: TYMS
REACTOME: TYMS
ConsensusPathDB
Pathway Commons: TYMS
MetabolismMetaCyc: TYMS
HUMANCyc: TYMS
RegulationEnsembl's Regulation: ENSG00000176890
miRBase: chr18 :657,603-673,499
TargetScan: NM_001071
cisRED: ENSG00000176890
ContextiHOP: TYMS
cancer metabolism search in PubMed: TYMS
UCL Cancer Institute: TYMS
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TYMS in cancer cell metabolism1. Huang M-Y, Wu C-H, Huang C-M, Chung F-Y, Huang C-W, et al. (2013) DPYD, TYMS, TYMP, TK1, and TK2 Genetic Expressions as Response Markers in Locally Advanced Rectal Cancer Patients Treated with Fluoropyrimidine-Based Chemoradiotherapy. BioMed research international 2013. go to article

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Phenotypic Information for TYMS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TYMS
Familial Cancer Database: TYMS
* 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_PYRIMIDINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM 188350; gene.
Orphanet 240839; 5-fluorouracil toxicity.
240855; Capecitabine toxicity.
240955; Susceptibility to adverse reaction due to 5-fluorouracil treatment.
240963; Susceptibility to adverse reaction due to capecitabine treatment.
DiseaseKEGG Disease: TYMS
MedGen: TYMS (Human Medical Genetics with Condition)
ClinVar: TYMS
PhenotypeMGI: TYMS (International Mouse Phenotyping Consortium)
PhenomicDB: TYMS

Mutations for TYMS
* 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 TYMS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW878210TYMS11613518668840668859TGIF2-C20orf24128323203524028835240483
DB026411TYMS133018660763661092TRAIP32556034987773549879334

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 # sample 2    1 1    11  
GAIN (# sample) 1      1    11  
LOSS (# sample) 1    1          
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)		Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr18:670707-670707p.A191V3
chr18:659673-659673p.F80L1
chr18:670725-670725p.A197D1
chr18:670822-670822p.S229R1
chr18:659694-659694p.E87K1
chr18:670729-670729p.L198L1
chr18:670827-670828p.A231D1
chr18:662242-662242p.R126G1
chr18:670738-670738p.F201L1
chr18:670835-670835p.T234A1

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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
# sample11 8  1  1 4     1 1
# mutation21 7  1  1 4     1 1
nonsynonymous SNV11 4  1  1 1     1  
synonymous SNV1  4       3       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
chr18:670822p.D173D2
chr18:669136p.S229S2
chr18:662243p.M149V1
chr18:670816p.R176K1
chr18:662311p.L198L1
chr18:670835p.Y202H1
chr18:669144p.V204V1
chr18:672957p.E207K1
chr18:670729p.L212L1
chr18:670739p.L212L1

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 TYMS 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 TYMS

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

AFG3L2,AURKB,CCNB2,CDC45,CDCA8,EZH2,FAM64A,
FOXM1,KIF23,KIF2C,KIF4A,KIFC1,MCM3,MCM7,
NDC80,ORC1,PHF19,RAD54L,SKA1,STMN1,TYMS		ASF1B,AURKB,CCNB1,CCNB2,CDCA3,CDCA5,CEP55,
DLGAP5,FOXM1,HJURP,KIAA0101,LMNB1,NDC80,NUSAP1,
ORC1,PBK,RAD51,RAD54L,SKA1,SKA3,TYMS

ATP5A1,TIMM21,TYMSOS,CENPM,CEP76,CHAF1B,DEPDC1,
MCM5,MCM6,NDC80,ORC1,PBK,RAD51,RFC5,
RRM2,SFXN1,SKA1,TUBA1B,TYMS,USP14,WDR76		ASF1B,CDCA5,CEP55,CHEK1,DIAPH3,ERCC6L,EXO1,
FANCI,FEN1,GINS4,MCM10,MELK,NCAPG,NCAPH,
ORC1,RAD54L,RRM2,SKA3,TK1,TRIP13,TYMS
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 TYMS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04818; -.
ChemistryChEMBL CHEMBL1952; -.
ChemistryGuidetoPHARMACOLOGY 2642; -.
Organism-specific databasesPharmGKB PA359; -.
Organism-specific databasesCTD 7298; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01099thymidylate synthetaseapprovedFlucytosine
DB00293thymidylate synthetaseapproved; investigationalRaltitrexed
DB00322thymidylate synthetaseapprovedFloxuridine
DB00432thymidylate synthetaseapprovedTrifluridine
DB00440thymidylate synthetaseapprovedTrimethoprim
DB00441thymidylate synthetaseapprovedGemcitabine
DB00544thymidylate synthetaseapprovedFluorouracil
DB00642thymidylate synthetaseapproved; investigationalPemetrexed
DB00650thymidylate synthetaseapprovedLeucovorin
DB01101thymidylate synthetaseapproved; investigationalCapecitabine
DB01643thymidylate synthetaseexperimentalThymidine-5'-Phosphate
DB03541thymidylate synthetaseexperimental10-Propargyl-5,8-Dideazafolic Acid
DB03800thymidylate synthetaseexperimental2'-deoxyuridylic acid
DB04530thymidylate synthetaseexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB07577thymidylate synthetaseexperimental6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE
DB08478thymidylate synthetaseexperimentalN-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide
DB08479thymidylate synthetaseexperimentalN-(3,5-dimethoxyphenyl)imidodicarbonimidic diamide
DB08734thymidylate synthetaseexperimental6,6-DIMETHYL-1-[3-(2,4,5-TRICHLOROPHENOXY)PROPOXY]-1,6-DIHYDRO-1,3,5-TRIAZINE-2,4-DIAMINE
DB02031thymidylate synthetaseexperimental(6s)-5,6,7,8-Tetrahydrofolate
DB02223thymidylate synthetaseexperimentalLy231514 Tetra Glu
DB02256thymidylate synthetaseexperimental2'-Deoxyuridine
DB02301thymidylate synthetaseexperimental5,10-Methylene-6-Hydrofolic Acid
DB02467thymidylate synthetaseexperimentalS-Oxymethionine
DB02752thymidylate synthetaseexperimentalTosyl-D-Proline
DB02899thymidylate synthetaseexperimentalN-Carboxymethionine
DB03038thymidylate synthetaseexperimentalLY341770
DB03157thymidylate synthetaseexperimentalN,O-Didansyl-L-Tyrosine
DB03274thymidylate synthetaseexperimental2'-5'dideoxyuridine
DB03558thymidylate synthetaseexperimentalSp-876
DB03761thymidylate synthetaseexperimental5-Fluoro-2'-Deoxyuridine-5'-Monophosphate
DB03818thymidylate synthetaseexperimentalN-[Tosyl-D-Prolinyl]Amino-Ethanethiol
DB04447thymidylate synthetaseexperimental1,4-Dithiothreitol
DB04457thymidylate synthetaseexperimental2'-Deoxyguanosine-5'-Monophosphate
DB04503thymidylate synthetaseexperimentalSp-722
DB04586thymidylate synthetaseexperimental2-bromophenol
DB04696thymidylate synthetaseexperimental4-CHLORO-3',3''-DIBROMOPHENOL-1,8-NAPHTHALEIN
DB08131thymidylate synthetaseexperimental2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-3-METHYL-BUTYRIC ACID
DB03685thymidylate synthetaseexperimentalUridine-5'-Monophosphate
DB03798thymidylate synthetaseexperimental2'-Deoxycytidine-5'-Monophosphate
DB06860thymidylate synthetaseexperimental2-(2-chloropyridin-4-yl)-4-methyl-1H-isoindole-1,3(2H)-dione
DB07507thymidylate synthetaseexperimental2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione
DB07511thymidylate synthetaseexperimental4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile
DB08204thymidylate synthetaseexperimental3-DIPHENOL-6-NITRO-3H-BENZO[DE]ISOCHROMEN-1-ONE
DB01234thymidylate synthetaseapproved; investigationalDexamethasone
DB00531thymidylate synthetaseapproved; investigationalCyclophosphamide
DB00970thymidylate synthetaseapprovedDactinomycin
DB00997thymidylate synthetaseapproved; investigationalDoxorubicin
DB01611thymidylate synthetaseapprovedHydroxychloroquine
DB00795thymidylate synthetaseapprovedSulfasalazine
DB00130thymidylate synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00515thymidylate synthetaseapprovedCisplatin
DB00115thymidylate synthetaseapproved; nutraceuticalCyanocobalamin
DB00158thymidylate synthetaseapproved; nutraceuticalFolic Acid
DB00165thymidylate synthetaseapproved; nutraceuticalPyridoxine
DB00526thymidylate synthetaseapproved; investigationalOxaliplatin
DB00987thymidylate synthetaseapproved; investigationalCytarabine
DB00694thymidylate synthetaseapprovedDaunorubicin
DB00773thymidylate synthetaseapprovedEtoposide
DB01033thymidylate synthetaseapprovedMercaptopurine
DB00563thymidylate synthetaseapprovedMethotrexate
DB00635thymidylate synthetaseapprovedPrednisone
DB00541thymidylate synthetaseapproved; investigationalVincristine
DB00762thymidylate synthetaseapproved; investigationalIrinotecan
DB01050thymidylate synthetaseapprovedIbuprofen
DB00958thymidylate synthetaseapprovedCarboplatin


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Cross referenced IDs for TYMS
* 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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