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 WWTR1
Basic gene info.Gene symbolWWTR1
Gene nameWW domain containing transcription regulator 1
SynonymsTAZ
CytomapUCSC genome browser: 3q23-q24
Genomic locationchr3 :149235021-149421060
Type of geneprotein-coding
RefGenesNM_001168278.1,
NM_001168280.1,NM_015472.4,
Ensembl idENSG00000018408
DescriptionWW domain-containing transcription regulator protein 1transcriptional co-activator with PDZ-binding motiftranscriptional coactivator with PDZ-binding motif
Modification date20141207
dbXrefs MIM : 607392
HGNC : HGNC
Ensembl : ENSG00000018408
HPRD : 09580
Vega : OTTHUMG00000159614
ProteinUniProt: Q9GZV5
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WWTR1
BioGPS: 25937
Gene Expression Atlas: ENSG00000018408
The Human Protein Atlas: ENSG00000018408
PathwayNCI Pathway Interaction Database: WWTR1
KEGG: WWTR1
REACTOME: WWTR1
ConsensusPathDB
Pathway Commons: WWTR1
MetabolismMetaCyc: WWTR1
HUMANCyc: WWTR1
RegulationEnsembl's Regulation: ENSG00000018408
miRBase: chr3 :149,235,021-149,421,060
TargetScan: NM_001168278
cisRED: ENSG00000018408
ContextiHOP: WWTR1
cancer metabolism search in PubMed: WWTR1
UCL Cancer Institute: WWTR1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for WWTR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 607392; gene.
Orphanet
DiseaseKEGG Disease: WWTR1
MedGen: WWTR1 (Human Medical Genetics with Condition)
ClinVar: WWTR1
PhenotypeMGI: WWTR1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryWWTR1chr3149257088149257288WWTR1chr3149276983149277183
ovaryWWTR1chr3149275503149275523chr3149068802149068822
ovaryWWTR1chr3149389010149389030WWTR1chr3149339224149339244
pancreasWWTR1chr3149255298149255318WWTR1chr3149255360149255380
pancreasWWTR1chr3149282154149282174WWTR1chr3149283008149283028
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows WWTR1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA311460WWTR1172933149238377149238653WWTR12904603149238671149243864

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 # sample2       3 2  3   
GAIN (# sample)2       3 2  2   
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=7

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check002.gifSomatic 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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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
chr3:149260151-149260151p.R248*5
chr3:149245633-149245633p.F299V5
chr3:149238728-149238728p.R356H3
chr3:149245664-149245664p.M288I2
chr3:149243902-149243902p.H306Y2
chr3:149245632-149245632p.F299S2
chr3:149260222-149260222p.A224V2
chr3:149238691-149238691p.N368N1
chr3:149290773-149290773p.I149N1
chr3:149245639-149245639p.D297N1

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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
# sample2116       442  52 5
# mutation2114       542  62 5
nonsynonymous SNV2  4       321  32 4
synonymous SNV 11        221  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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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
chr3:149260222p.F299S,WWTR12
chr3:149245632p.F299L,WWTR12
chr3:149245633p.A224V,WWTR12
chr3:149238729p.R356S,WWTR11
chr3:149260194p.P178S,WWTR11
chr3:149290773p.Q353H,WWTR11
chr3:149238736p.V172V,WWTR11
chr3:149374727p.I350I,WWTR11
chr3:149238745p.V172I,WWTR11
chr3:149260244p.G303G,WWTR11

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 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

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.
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check002.gifProtein 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.

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

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
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 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



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