Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 TPK1
Basic gene info.Gene symbolTPK1
Gene namethiamin pyrophosphokinase 1
SynonymsHTPK1|PP20|THMD5
CytomapUCSC genome browser: 7q34-q35
Genomic locationchr7 :144149033-144533146
Type of geneprotein-coding
RefGenesNM_001042482.1,
NM_022445.3,
Ensembl idENSG00000196511
Descriptionplacental protein 20thiamine diphosphokinasethiamine kinase
Modification date20141207
dbXrefs MIM : 606370
HGNC : HGNC
Ensembl : ENSG00000196511
HPRD : 06967
Vega : OTTHUMG00000152774
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPK1
BioGPS: 27010
Gene Expression Atlas: ENSG00000196511
The Human Protein Atlas: ENSG00000196511
PathwayNCI Pathway Interaction Database: TPK1
KEGG: TPK1
REACTOME: TPK1
ConsensusPathDB
Pathway Commons: TPK1
MetabolismMetaCyc: TPK1
HUMANCyc: TPK1
RegulationEnsembl's Regulation: ENSG00000196511
miRBase: chr7 :144,149,033-144,533,146
TargetScan: NM_001042482
cisRED: ENSG00000196511
ContextiHOP: TPK1
cancer metabolism search in PubMed: TPK1
UCL Cancer Institute: TPK1
Assigned class in ccmGDBC

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Phenotypic Information for TPK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TPK1
Familial Cancer Database: TPK1
* 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
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TPK1
MedGen: TPK1 (Human Medical Genetics with Condition)
ClinVar: TPK1
PhenotypeMGI: TPK1 (International Mouse Phenotyping Consortium)
PhenomicDB: TPK1

Mutations for TPK1
* 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
ovaryTPK1chr7144164181144164201TPK1chr7144226274144226294
ovaryTPK1chr7144474466144474486chr23137691123137691143
ovaryTPK1chr7144477427144477447ADKchr107625071476250734
ovaryTPK1chr7144483786144483806chr7144549781144549801
pancreasTPK1chr7144491885144491905TPK1chr7144493829144493849
pancreasTPK1chr7144497186144497206TPK1chr7144499920144499940
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 TPK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM459600TPK151127144343977144344086CYCS10419372516245325162542
EC547646ZCCHC17187613181953031819588TPK1771087144271457144271962

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 1 11   2 2  4   
GAIN (# sample) 1 1    2 2  4   
LOSS (# sample)    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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr7:144320303-144320303p.C104R4
chr7:144288554-144288554p.I155V2
chr7:144150652-144150652p.A240T2
chr7:144380014-144380014p.G58E2
chr7:144288563-144288563p.P152T2
chr7:144380018-144380018p.E57K2
chr7:144380045-144380045p.G48C2
chr7:144245631-144245631p.G189V1
chr7:144345919-144345919p.R80I1
chr7:144288534-144288534p.L161L1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 9  3 11 652  114 3
# mutation11 8  3 11 652  114 3
nonsynonymous SNV11 7  3 11 652  84 3
synonymous SNV   1            3   
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
chr7:144320303p.C104R,TPK14
chr7:144288620p.A191T,TPK12
chr7:144150652p.I155V2
chr7:144380014p.G58V,TPK12
chr7:144380018p.D133N2
chr7:144288554p.E57K,TPK12
chr7:144245652p.W133L,TPK11
chr7:144150649p.K111M,TPK11
chr7:144320338p.G128E,TPK11
chr7:144245667p.Q109K,TPK11

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 TPK1 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 TPK1

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

ARHGEF16,B3GNT7,BPIFB3,TOR4A,CPVL,DISC1,F5,
KCTD14,MEIS2,PANK4,PDIA2,PIK3AP1,QSOX1,RER1,
SKI,SMR3A,SMR3B,TESC,TMX4,TPK1,TRAF4
ATP6V1B2,BCAT1,CCDC109B,CLIC2,CPVL,CTSC,DAB2,
FAP,GALNT12,GPNMB,HEXB,HPGDS,HRH1,LPAR1,
LY96,MAF,MFSD1,MS4A6A,RAB23,SLC38A6,TPK1

C11orf86,C4orf19,CA2,CA4,CASP5,CCL28,CEACAM7,
CHMP2B,CLCA4,DHRS9,EDN3,GUCA2B,MALL,MYPN,
PLAC8,PTPRH,RHOC,SDCBP2,SMPDL3A,TPK1,TSPAN1
ASS1,C4BPB,CD164L2,CLEC6A,CXCL1,DUOXA2,GRAMD2,
GRHL3,LCN2,LYPD5,MMP1,NOS2,PI3,PLA2G2A,
RTEL1,SLC6A14,TNFRSF6B,TNFSF12-TNFSF13,TPK1,TRIM40,TSPO2
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 TPK1
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
DB00152thiamin pyrophosphokinase 1approved; nutraceuticalThiamine
DB04768thiamin pyrophosphokinase 1experimentalPyrithiamine Pyrophosphate


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Cross referenced IDs for TPK1
* 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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