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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	TPK1
	Gene name	thiamin pyrophosphokinase 1
	Synonyms	HTPK1\|PP20\|THMD5
	Cytomap	UCSC genome browser: 7q34-q35
	Genomic location	chr7 :144149033-144533146
	Type of gene	protein-coding
	RefGenes	NM_001042482.1, NM_022445.3,
	Ensembl id	ENSG00000196511
	Description	placental protein 20thiamine diphosphokinasethiamine kinase
	Modification date	20141207
dbXrefs	MIM : 606370
	HGNC : HGNC
	Ensembl : ENSG00000196511
	HPRD : 06967
	Vega : OTTHUMG00000152774
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TPK1
	BioGPS: 27010
	Gene Expression Atlas: ENSG00000196511
	The Human Protein Atlas: ENSG00000196511
Pathway	NCI Pathway Interaction Database: TPK1
	KEGG: TPK1
	REACTOME: TPK1
	ConsensusPathDB
	Pathway Commons: TPK1
Metabolism	MetaCyc: TPK1
	HUMANCyc: TPK1
Regulation	Ensembl's Regulation: ENSG00000196511
	miRBase: chr7 :144,149,033-144,533,146
	TargetScan: NM_001042482
	cisRED: ENSG00000196511
Context	iHOP: TPK1
	cancer metabolism search in PubMed: TPK1
	UCL Cancer Institute: TPK1
Assigned class in ccmGDB	C

Top

Phenotypic Information for TPK1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

Others
OMIM
Orphanet
Disease	KEGG Disease: TPK1
	MedGen: TPK1 (Human Medical Genetics with Condition)
	ClinVar: TPK1
Phenotype	MGI: TPK1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	TPK1	chr7	144164181	144164201	TPK1	chr7	144226274	144226294
ovary	TPK1	chr7	144474466	144474486		chr23	137691123	137691143
ovary	TPK1	chr7	144477427	144477447	ADK	chr10	76250714	76250734
ovary	TPK1	chr7	144483786	144483806		chr7	144549781	144549801
pancreas	TPK1	chr7	144491885	144491905	TPK1	chr7	144493829	144493849
pancreas	TPK1	chr7	144497186	144497206	TPK1	chr7	144499920	144499940

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TPK1 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
BM459600	TPK1	5	112	7	144343977	144344086	CYCS	104	193	7	25162453	25162542
EC547646	ZCCHC17	18	76	1	31819530	31819588	TPK1	77	108	7	144271457	144271962

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=6

Top

Somatic 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.

Top

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
chr7:144320303-144320303	p.C104R	4
chr7:144288554-144288554	p.I155V	2
chr7:144150652-144150652	p.A240T	2
chr7:144380014-144380014	p.G58E	2
chr7:144288563-144288563	p.P152T	2
chr7:144380018-144380018	p.E57K	2
chr7:144380045-144380045	p.G48C	2
chr7:144245694-144245694	p.G168E	1
chr7:144463012-144463012	p.Q26*	1
chr7:144320258-144320258	p.?	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		9			3		1	1		6	5	2			11	4		3
# mutation	1	1		8			3		1	1		6	5	2			11	4		3
nonsynonymous SNV	1	1		7			3		1	1		6	5	2			8	4		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])

Top

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
chr7:144320303	p.C104R,TPK1	4
chr7:144288554	p.A191T,TPK1	2
chr7:144288620	p.I155V	2
chr7:144150652	p.G58V,TPK1	2
chr7:144380014	p.D133N	2
chr7:144380018	p.E57K,TPK1	2
chr7:144320302	p.W133L,TPK1	1
chr7:144245644	p.K111M,TPK1	1
chr7:144463037	p.G128E,TPK1	1
chr7:144288563	p.Q109K,TPK1	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 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]

Top

Gene Expression for TPK1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


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

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for TPK1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00152	thiamin pyrophosphokinase 1	approved; nutraceutical	Thiamine
DB04768	thiamin pyrophosphokinase 1	experimental	Pyrithiamine Pyrophosphate

Top

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