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 WWTR1

Basic gene info.	Gene symbol	WWTR1
	Gene name	WW domain containing transcription regulator 1
	Synonyms	TAZ
	Cytomap	UCSC genome browser: 3q23-q24
	Genomic location	chr3 :149235021-149421060
	Type of gene	protein-coding
	RefGenes	NM_001168278.1, NM_001168280.1,NM_015472.4,
	Ensembl id	ENSG00000018408
	Description	WW domain-containing transcription regulator protein 1transcriptional co-activator with PDZ-binding motiftranscriptional coactivator with PDZ-binding motif
	Modification date	20141207
dbXrefs	MIM : 607392
	HGNC : HGNC
	Ensembl : ENSG00000018408
	HPRD : 09580
	Vega : OTTHUMG00000159614
Protein	UniProt: Q9GZV5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_WWTR1
	BioGPS: 25937
	Gene Expression Atlas: ENSG00000018408
	The Human Protein Atlas: ENSG00000018408
Pathway	NCI Pathway Interaction Database: WWTR1
	KEGG: WWTR1
	REACTOME: WWTR1
	ConsensusPathDB
	Pathway Commons: WWTR1
Metabolism	MetaCyc: WWTR1
	HUMANCyc: WWTR1
Regulation	Ensembl's Regulation: ENSG00000018408
	miRBase: chr3 :149,235,021-149,421,060
	TargetScan: NM_001168278
	cisRED: ENSG00000018408
Context	iHOP: WWTR1
	cancer metabolism search in PubMed: WWTR1
	UCL Cancer Institute: WWTR1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for WWTR1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: WWTR1
	Familial Cancer Database: WWTR1

* 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_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	607392; gene.
Orphanet
Disease	KEGG Disease: WWTR1
	MedGen: WWTR1 (Human Medical Genetics with Condition)
	ClinVar: WWTR1
Phenotype	MGI: WWTR1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: WWTR1

Mutations for WWTR1

* 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
ovary	WWTR1	chr3	149257088	149257288	WWTR1	chr3	149276983	149277183
ovary	WWTR1	chr3	149275503	149275523		chr3	149068802	149068822
ovary	WWTR1	chr3	149389010	149389030	WWTR1	chr3	149339224	149339244
pancreas	WWTR1	chr3	149255298	149255318	WWTR1	chr3	149255360	149255380
pancreas	WWTR1	chr3	149282154	149282174	WWTR1	chr3	149283008	149283028

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 WWTR1 related fusion information.

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

CA311460

WWTR1

293

149238377

149238653

WWTR1

290

460

149238671

149243864

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=37)	Stat. for Synonymous SNVs (# total SNVs=8)

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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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
chr3:149245633-149245633	p.F299V	5
chr3:149260151-149260151	p.R248*	5
chr3:149238728-149238728	p.R356H	3
chr3:149245632-149245632	p.F299S	2
chr3:149260222-149260222	p.A224V	2
chr3:149245664-149245664	p.M288I	2
chr3:149243902-149243902	p.H306Y	2
chr3:149243909-149243909	p.G303G	1
chr3:149374873-149374873	p.P74Q	1
chr3:149260194-149260194	p.Q233H	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	1	1	6								4	4	2			5	2		5
# mutation	2	1	1	4								5	4	2			6	2		5
nonsynonymous SNV	2			4								3	2	1			3	2		4
synonymous SNV		1	1									2	2	1			3			1

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
chr3:149260222	p.A224V,WWTR1	2
chr3:149245632	p.F299S,WWTR1	2
chr3:149245633	p.F299L,WWTR1	2
chr3:149245664	p.K54Q,WWTR1	1
chr3:149290715	p.G217R,WWTR1	1
chr3:149374963	p.R44R,WWTR1	1
chr3:149245727	p.S202I,WWTR1	1
chr3:149290738	p.R44L,WWTR1	1
chr3:149375082	p.S185S,WWTR1	1
chr3:149260187	p.A4A,WWTR1	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 WWTR1 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 WWTR1

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


ANKRD36BP1,CALU,CHST3,COMMD2,CREB3L2,CTTNBP2NL,DDR2, FNDC3B,KIAA0754,MAML2,MRAS,MSN,PLS3,PRICKLE1, PTPN14,QKI,STK38L,WWTR1,YEATS2,ZNF462,ZNF532	GPATCH2L,ERCC6L2,CDK12,FAM168A,JMJD1C,LATS1,LRCH3, LRP6,NIPAL2,NUP153,NUP160,PDZD8,PPP4R2,RANBP2, RASA2,ROR1,SON,TCF12,WWTR1,ZDHHC20,ZNF426

AXL,C1R,CCDC88A,CEP170,CFH,CHST15,DDR2, EHD2,ELK3,FAM129A,KIAA1462,KLHL5,NRP1,NRP2, NXN,OSMR,PKD2,PTPRM,PTRF,WWTR1,ZNF532	AKT3,AMOTL1,C16orf45,FAXC,DMD,EML1,FILIP1, FOXP2,ICA1L,KANK2,PALLD,PARVA,PPP1R12B,PRKG1, RAB9B,SCN7A,SOBP,SORBS1,SORBS2,TEAD1,WWTR1

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 WWTR1

There's no related Drug.

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Cross referenced IDs for WWTR1

* 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