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 TKT
Basic gene info.Gene symbolTKT
Gene nametransketolase
SynonymsHEL107|TK|TKT1
CytomapUCSC genome browser: 3p14.3
Genomic locationchr3 :53259652-53290130
Type of geneprotein-coding
RefGenesNM_001064.3,
NM_001135055.2,NM_001258028.1,NR_047580.1,NM_001135056.1,
NR_047579.1,
Ensembl idENSG00000163931
Descriptionepididymis luminal protein 107
Modification date20141211
dbXrefs MIM : 606781
HGNC : HGNC
Ensembl : ENSG00000163931
HPRD : 06001
Vega : OTTHUMG00000158192
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TKT
BioGPS: 7086
Gene Expression Atlas: ENSG00000163931
The Human Protein Atlas: ENSG00000163931
PathwayNCI Pathway Interaction Database: TKT
KEGG: TKT
REACTOME: TKT
ConsensusPathDB
Pathway Commons: TKT
MetabolismMetaCyc: TKT
HUMANCyc: TKT
RegulationEnsembl's Regulation: ENSG00000163931
miRBase: chr3 :53,259,652-53,290,130
TargetScan: NM_001064
cisRED: ENSG00000163931
ContextiHOP: TKT
cancer metabolism search in PubMed: TKT
UCL Cancer Institute: TKT
Assigned class in ccmGDBC

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

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

Mutations for TKT
* 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 TKT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF349570TKT214335326207953262347TKT14126735325991853260868
BF002266CDC377107191050180910501909TKT10741235326906953275233
BF529930TKT349835326209053262154TKT9853435325967053262106
BE741860TKT157435326081353264500YLPM1575658147526935475276140
CD388242RPL114130212401909824020406TKT30238635325966853259752
BE740522TKT157735326081253264500YLPM1578831147526935475276330
BG488822TKT156935326540853265462TKT6387035326077953265422
BI094438TKT4311235325974453259813TKT11021735325966453259771
AW847418TKT66335326714553267203TKT6315935326740053267497
AW880069TKT49835325976953259866CPXM29011110125537690125537711

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   1  
GAIN (# sample)          1      
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr3:53262297-53262297p.A492S2
chr3:53269121-53269121p.F169F2
chr3:53263300-53263300p.S420S2
chr3:53264616-53264616p.G322R2
chr3:53263350-53263350p.A404T2
chr3:53260781-53260781p.Y563H2
chr3:53263040-53263040p.L460I1
chr3:53275202-53275202p.A95A1
chr3:53263430-53263430p.A377V1
chr3:53260860-53260860p.T536T1

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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 2 9  1 11 2 2 173 9
# mutation 2 9  1 11 2 2 173 10
nonsynonymous SNV 2 6  1 11 2 2 133 7
synonymous SNV   3            4  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
chr3:53263300p.S420S,TKT2
chr3:53263350p.Y563H,TKT2
chr3:53260781p.A404T,TKT2
chr3:53276233p.A45T,TKT2
chr3:53263147p.T536T,TKT1
chr3:53269001p.H330H,TKT1
chr3:53260829p.V531M,TKT1
chr3:53269083p.R318H,TKT1
chr3:53260860p.K523N,TKT1
chr3:53263320p.P263S,TKT1

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 TKT 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 TKT

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

ALDH3A1,BCL2L10,C7orf33,CDHR2,GAGE12J,GAGE13,GAGE2B,
GAGE8,GPX2,IQCF2,LOC285629,NKX2-4,PYY2,RBMXL2,
TKTL1,TPH1,UGT1A5,UPK3B,VCX,VCX3A,VCY
ADAP2,AIF1,ARPC2,ATP1B3,CTSC,ECSCR,FKBP1A,
FLI1,GLRX,GNG11,ITGAE,LMO2,LY96,NTAN1,
PECAM1,PPAP2A,RALB,TKTL1,TPST2,UBE2A,VOPP1

C2orf82,CADM2,CDH22,CPLX2,CPNE9,DMRT3,FSD1,
GLYATL3,HULC,INHBB,KCNK16,KIAA1257,LOC441454,MAGEA9B,
NOTUM,NTS,PLA2G2E,TBX4,TDRD1,TKTL1,ZNF556
APOL4,C3orf79,CCL2,CD274,CXCL10,FCGR1A,FCGR1B,
FCGR1C,HAPLN3,IDO1,IL27,LHX8,LOC400696,LOC400759,
MNDA,PAQR9,PER4,SCGB1D4,SEPT14,TKTL1,VAMP5
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 TKT


There's no related Drug.
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Cross referenced IDs for TKT
* 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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