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 TK1
Basic gene info.Gene symbolTK1
Gene namethymidine kinase 1, soluble
SynonymsTK2
CytomapUCSC genome browser: 17q23.2-q25.3
Genomic locationchr17 :76170159-76183285
Type of geneprotein-coding
RefGenesNM_003258.4,
Ensembl idENSG00000167900
Descriptionthymidine kinase 1 soluble isoformthymidine kinase, cytosolicthymidine kinase-1
Modification date20141207
dbXrefs MIM : 188300
HGNC : HGNC
Ensembl : ENSG00000167900
HPRD : 01771
Vega : OTTHUMG00000150674
ProteinUniProt: P04183
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TK1
BioGPS: 7083
Gene Expression Atlas: ENSG00000167900
The Human Protein Atlas: ENSG00000167900
PathwayNCI Pathway Interaction Database: TK1
KEGG: TK1
REACTOME: TK1
ConsensusPathDB
Pathway Commons: TK1
MetabolismMetaCyc: TK1
HUMANCyc: TK1
RegulationEnsembl's Regulation: ENSG00000167900
miRBase: chr17 :76,170,159-76,183,285
TargetScan: NM_003258
cisRED: ENSG00000167900
ContextiHOP: TK1
cancer metabolism search in PubMed: TK1
UCL Cancer Institute: TK1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TK1 in cancer cell metabolism1. Brockenbrough JS, Morihara JK, Hawes SE, Stern JE, Rasey JS, et al. (2009) Thymidine kinase 1 and thymidine phosphorylase expression in non-small-cell lung carcinoma in relation to angiogenesis and proliferation. Journal of Histochemistry & Cytochemistry 57: 1087-1097. go to article
2. O’Brien PJ, Lee M, Spilker ME, Zhang CC, Yan Z, et al. (2013) Monitoring metabolic responses to chemotherapy in single cells and tumors using nanostructure-initiator mass spectrometry (NIMS) imaging. Cancer & metabolism 1: 1-14. go to article

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Phenotypic Information for TK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TK1
Familial Cancer Database: TK1
* 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
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM 188300; gene.
Orphanet
DiseaseKEGG Disease: TK1
MedGen: TK1 (Human Medical Genetics with Condition)
ClinVar: TK1
PhenotypeMGI: TK1 (International Mouse Phenotyping Consortium)
PhenomicDB: TK1

Mutations for TK1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryTK1chr177617128576171305chr222419830324198323
pancreasTK1chr177617136376171383RECQL5chr177363523073635250
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE729700UBTF1125174228335942283484TK1124714177617109776183116
AW376086CALCOCO121315125410502054105313TK1307671177617659776176963
BG118054TK125237177617052076170734CAMTA1236304171005967215212

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 # sample1         1      
GAIN (# sample)1         1      
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=9)
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
chr17:76170965-76170965p.S194P1
chr17:76178728-76178728p.R82Q1
chr17:76170993-76170993p.V184V1
chr17:76178748-76178748p.A75A1
chr17:76171137-76171137p.E169E1
chr17:76181214-76181214p.Q44L1
chr17:76171139-76171139p.E169K1
chr17:76171144-76171144p.G167D1
chr17:76171214-76171214p.E144K1
chr17:76171626-76171626p.G126V1

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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
# sample1  1             224
# mutation2  1             224
nonsynonymous SNV1  1             223
synonymous SNV1                  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
chr17:76170933p.S194P1
chr17:76170965p.V184V1
chr17:76170993p.E169E1
chr17:76171137p.E169K1
chr17:76171139p.G167D1
chr17:76171144p.G116R1
chr17:76171657p.D83E1
chr17:76178724p.A78T1
chr17:76178741p.A233T1
chr17:76170848p.K211T1

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 TK1 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 TK1

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

BIRC5,C17orf89,CCDC137,CENPM,DUS1L,EPR1,GJA10,
GPS1,HCCS,JMJD6,MRPL12,MRPL38,P4HB,PCYT2,
PIR,PKMYT1,SLC25A10,STRA13,SYNGR2,ALYREF,TK1
ASF1B,BIRC5,CDC45,CDCA5,CENPM,E2F1,EPR1,
FAM111B,FEN1,GALE,KIFC1,PKMYT1,POC1A,PYCR1,
RAD51,RAD54L,RECQL4,RRM2,TK1,UHRF1,ZWINT

ASF1B,BIRC5,C17orf53,CDC45,CENPM,EIF4A3,EPR1,
FEN1,H2AFX,HAUS8,LRRC59,MCM5,MRPL27,RAD51,
RRM2,SLC25A19,STRA13,ALYREF,TK1,TUBA1B,WDR34
ASF1B,CDCA5,CDCA8,CENPM,CEP55,CHAF1B,EXO1,
FEN1,GINS4,MELK,NCAPH,OIP5,ORC1,POC1A,
RAD54L,RNASEH2A,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 TK1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04183; -.
ChemistryChEMBL CHEMBL2883; -.
Organism-specific databasesPharmGKB PA352; -.
Organism-specific databasesCTD 7083; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01692thymidine kinase 1, solubleexperimentalDithioerythritol
DB02452thymidine kinase 1, solubleexperimentalThymidine-5'-Triphosphate
DB01101thymidine kinase 1, solubleapproved; investigationalCapecitabine
DB00544thymidine kinase 1, solubleapprovedFluorouracil
DB02745thymidine kinase 1, solubleexperimentalUridine
DB00495thymidine kinase 1, solubleapprovedZidovudine
DB01033thymidine kinase 1, solubleapprovedMercaptopurine
DB00563thymidine kinase 1, solubleapprovedMethotrexate
DB01050thymidine kinase 1, solubleapprovedIbuprofen


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Cross referenced IDs for TK1
* 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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