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 TNKS1BP1

Basic gene info.	Gene symbol	TNKS1BP1
	Gene name	tankyrase 1 binding protein 1, 182kDa
	Synonyms	TAB182
	Cytomap	UCSC genome browser: 11q12.1
	Genomic location	chr11 :57067102-57092413
	Type of gene	protein-coding
	RefGenes	NM_033396.2,
	Ensembl id	ENSG00000149115
	Description	182 kDa tankyrase-1-binding proteintankyrase 1-binding protein of 182 kDa
	Modification date	20141207
dbXrefs	MIM : 607104
	HGNC : HGNC
	Ensembl : ENSG00000149115
	HPRD : 06164
	Vega : OTTHUMG00000167022
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TNKS1BP1
	BioGPS: 85456
	Gene Expression Atlas: ENSG00000149115
	The Human Protein Atlas: ENSG00000149115
Pathway	NCI Pathway Interaction Database: TNKS1BP1
	KEGG: TNKS1BP1
	REACTOME: TNKS1BP1
	ConsensusPathDB
	Pathway Commons: TNKS1BP1
Metabolism	MetaCyc: TNKS1BP1
	HUMANCyc: TNKS1BP1
Regulation	Ensembl's Regulation: ENSG00000149115
	miRBase: chr11 :57,067,102-57,092,413
	TargetScan: NM_033396
	cisRED: ENSG00000149115
Context	iHOP: TNKS1BP1
	cancer metabolism search in PubMed: TNKS1BP1
	UCL Cancer Institute: TNKS1BP1
Assigned class in ccmGDB	C

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Phenotypic Information for TNKS1BP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TNKS1BP1
	Familial Cancer Database: TNKS1BP1

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: TNKS1BP1
	MedGen: TNKS1BP1 (Human Medical Genetics with Condition)
	ClinVar: TNKS1BP1
Phenotype	MGI: TNKS1BP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TNKS1BP1

Mutations for TNKS1BP1

* 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

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- 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
pancreas	TNKS1BP1	chr11	57070857	57070877	OR5AK2	chr11	56756813	56756833

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 TNKS1BP1 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
BF810602	TNKS1BP1	2	202	11	57077167	57077371	MACF1	198	363	1	39802872	39806207
BG436080	TNKS1BP1	1	106	11	57083289	57083394	PSG3	102	672	19	43407538	43411312
BF812770	ZNF207	18	156	17	30700470	30700610	TNKS1BP1	142	380	11	57074938	57075174
BF844047	FHL2	82	103	2	106025408	106025429	TNKS1BP1	92	356	11	57067207	57067473
BF950679	NLGN3	5	401	X	70390280	70390675	TNKS1BP1	390	583	11	57076478	57076671
BF838059	ANKDD1A	22	122	15	65218757	65218859	TNKS1BP1	111	216	11	57067297	57067402
BF756786	IGFBP4	1	248	17	38613640	38613889	TNKS1BP1	246	402	11	57076360	57076516
AV704306	TNKS1BP1	1	499	11	57075094	57075591	LRCH4	496	614	7	100172283	100172403
BM693293	TNKS1BP1	1	142	11	57075020	57075161	XCR1	134	201	3	46066340	46066411

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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=114)	Stat. for Synonymous SNVs (# total SNVs=38)

Stat. for Deletions (# total SNVs=7)	Stat. for Insertions (# total SNVs=1)

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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
chr11:57077353-57077353	p.A944A	7
chr11:57081197-57081197	p.T322S	3
chr11:57080736-57080736	p.F476I	3
chr11:57077354-57077354	p.A944G	2
chr11:57076529-57076529	p.G1219fs*15	2
chr11:57080907-57080907	p.R419C	2
chr11:57089263-57089263	p.?	2
chr11:57069988-57069988	p.R1543Q	2
chr11:57087724-57087724	p.R186H	2
chr11:57076793-57076793	p.R1131I	2

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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	7	6		22			7		8	3		16	10	3		1	20	11	1	15
# mutation	7	6		26			7		8	3		17	12	3		1	25	13	1	19
nonsynonymous SNV	5	5		16			5		7	2		13	9	3		1	19	11		13
synonymous SNV	2	1		10			2		1	1		4	3				6	2	1	6

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
chr11:57077271	p.S955S	2
chr11:57077309	p.T607T	2
chr11:57077320	p.R1131T	2
chr11:57080341	p.P604R	2
chr11:57080351	p.A898V	2
chr11:57087724	p.R186H	2
chr11:57077492	p.A972T	2
chr11:57076793	p.R959K	2
chr11:57080210	p.R389Q	1
chr11:57068382	p.Q1351H	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 TNKS1BP1 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 TNKS1BP1

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


AGRN,C11orf31,C9orf69,CCDC9,CLP1,EHD1,FAM73B, INTS5,MAP3K11,MED19,OSBPL5,PBXIP1,PLCB3,PLXNB2, RAB43,SIX5,TIMM10,TNKS1BP1,TSPAN9,ZBTB7B,ZDHHC5	AKT1,DDAH2,EGLN2,EML3,KIFC3,LRPAP1,MEGF8, MUM1,OS9,PFKL,PLCB3,PPP1R12C,RAB35,SDF4, SLC38A10,SLC4A2,SUN2,TAOK2,TMEM129,TNIP2,TNKS1BP1

AHDC1,AHNAK,AKAP13,ARHGAP1,CIC,GLG1,GOLGA2, HSPG2,IL4R,KDM2A,KIAA0247,MKL1,MYH9,RAI1, RAPGEF3,SH3PXD2A,SLC9A3R2,SUN2,TECPR1,TNKS1BP1,TRIM8	AGRN,ANKRD11,ANKRD52,BRD4,FBXL19,GTF3C1,KDM2A, LARP1,MCM3AP,KMT2B___KMT2D,MUC4,PHRF1,SEC16A,SMARCA4, SPEN,SRCAP,TAOK2,TNKS1BP1,TRIM56,TRRAP,VPS13D

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 TNKS1BP1

There's no related Drug.

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Cross referenced IDs for TNKS1BP1

* 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