Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 TKT

Basic gene info.	Gene symbol	TKT
	Gene name	transketolase
	Synonyms	HEL107\|TK\|TKT1
	Cytomap	UCSC genome browser: 3p14.3
	Genomic location	chr3 :53259652-53290130
	Type of gene	protein-coding
	RefGenes	NM_001064.3, NM_001135055.2,NM_001258028.1,NR_047580.1,NM_001135056.1, NR_047579.1,
	Ensembl id	ENSG00000163931
	Description	epididymis luminal protein 107
	Modification date	20141211
dbXrefs	MIM : 606781
	HGNC : HGNC
	Ensembl : ENSG00000163931
	HPRD : 06001
	Vega : OTTHUMG00000158192
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TKT
	BioGPS: 7086
	Gene Expression Atlas: ENSG00000163931
	The Human Protein Atlas: ENSG00000163931
Pathway	NCI Pathway Interaction Database: TKT
	KEGG: TKT
	REACTOME: TKT
	ConsensusPathDB
	Pathway Commons: TKT
Metabolism	MetaCyc: TKT
	HUMANCyc: TKT
Regulation	Ensembl's Regulation: ENSG00000163931
	miRBase: chr3 :53,259,652-53,290,130
	TargetScan: NM_001064
	cisRED: ENSG00000163931
Context	iHOP: TKT
	cancer metabolism search in PubMed: TKT
	UCL Cancer Institute: TKT
Assigned class in ccmGDB	C

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Phenotypic Information for TKT(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: TKT
	MedGen: TKT (Human Medical Genetics with Condition)
	ClinVar: TKT
Phenotype	MGI: TKT (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TKT related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BF349570	TKT	2	143	3	53262079	53262347	TKT	141	267	3	53259918	53260868
BF002266	CDC37	7	107	19	10501809	10501909	TKT	107	412	3	53269069	53275233
BF529930	TKT	34	98	3	53262090	53262154	TKT	98	534	3	53259670	53262106
BE741860	TKT	1	574	3	53260813	53264500	YLPM1	575	658	14	75269354	75276140
CD388242	RPL11	41	302	1	24019098	24020406	TKT	302	386	3	53259668	53259752
BE740522	TKT	1	577	3	53260812	53264500	YLPM1	578	831	14	75269354	75276330
BG488822	TKT	15	69	3	53265408	53265462	TKT	63	870	3	53260779	53265422
BI094438	TKT	43	112	3	53259744	53259813	TKT	110	217	3	53259664	53259771
AW847418	TKT	6	63	3	53267145	53267203	TKT	63	159	3	53267400	53267497
AW880069	TKT	4	98	3	53259769	53259866	CPXM2	90	111	10	125537690	125537711

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr3:53263350-53263350	p.A404T	2
chr3:53260781-53260781	p.Y563H	2
chr3:53262297-53262297	p.A492S	2
chr3:53269121-53269121	p.F169F	2
chr3:53263300-53263300	p.S420S	2
chr3:53264616-53264616	p.G322R	2
chr3:53263321-53263321	p.C413C	1
chr3:53259944-53259944	p.G567D	1
chr3:53265526-53265526	p.P263P	1
chr3:53263034-53263034	p.A462T	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		2		9			1		1	1		2		2		1	7	3		9
# mutation		2		9			1		1	1		2		2		1	7	3		10
nonsynonymous SNV		2		6			1		1	1		2		2		1	3	3		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:53260781	p.Y563H,TKT	2
chr3:53276233	p.A404T,TKT	2
chr3:53263300	p.A45T,TKT	2
chr3:53263350	p.S420S,TKT	2
chr3:53264627	p.A84T,TKT	1
chr3:53275237	p.I556I,TKT	1
chr3:53263106	p.A377V,TKT	1
chr3:53265528	p.R550C,TKT	1
chr3:53260800	p.A373V,TKT	1
chr3:53263130	p.S25R,TKT	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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