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 YAP1
Basic gene info.Gene symbolYAP1
Gene nameYes-associated protein 1
SynonymsCOB1|YAP|YAP2|YAP65|YKI
CytomapUCSC genome browser: 11q13
Genomic locationchr11 :101981191-102104154
Type of geneprotein-coding
RefGenesNM_001130145.2,
NM_001195044.1,NM_001195045.1,NM_001282097.1,NM_001282098.1,
NM_001282099.1,NM_001282100.1,NM_001282101.1,NM_006106.4,
Ensembl idENSG00000137693
Description65 kDa Yes-associated proteinprotein yorkie homologtranscriptional coactivator YAP1yes-associated protein 2yes-associated protein YAP65 homologyorkie homolog
Modification date20141222
dbXrefs MIM : 606608
HGNC : HGNC
Ensembl : ENSG00000137693
HPRD : 09424
Vega : OTTHUMG00000167322
ProteinUniProt: P46937
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_YAP1
BioGPS: 10413
Gene Expression Atlas: ENSG00000137693
The Human Protein Atlas: ENSG00000137693
PathwayNCI Pathway Interaction Database: YAP1
KEGG: YAP1
REACTOME: YAP1
ConsensusPathDB
Pathway Commons: YAP1
MetabolismMetaCyc: YAP1
HUMANCyc: YAP1
RegulationEnsembl's Regulation: ENSG00000137693
miRBase: chr11 :101,981,191-102,104,154
TargetScan: NM_001130145
cisRED: ENSG00000137693
ContextiHOP: YAP1
cancer metabolism search in PubMed: YAP1
UCL Cancer Institute: YAP1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of YAP1 in cancer cell metabolism1. Mapelli V, Hillestrøm PR, Patil K, Larsen EH, Olsson L (2012) The interplay between sulphur and selenium metabolism influences the intracellular redox balance in Saccharomyces cerevisiae. FEMS yeast research 12: 20-32. go to article

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Phenotypic Information for YAP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: YAP1
Familial Cancer Database: YAP1
* 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 120433; phenotype.
120433; phenotype.
606608; gene.
606608; gene.
Orphanet 1473; Uveal coloboma - cleft lip and palate - intellectual disability.
1473; Uveal coloboma - cleft lip and palate - intellectual disability.
DiseaseKEGG Disease: YAP1
MedGen: YAP1 (Human Medical Genetics with Condition)
ClinVar: YAP1
PhenotypeMGI: YAP1 (International Mouse Phenotyping Consortium)
PhenomicDB: YAP1

Mutations for YAP1
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryYAP1chr11102014722102014742YAP1chr11102015522102015542
ovaryYAP1chr11102027028102027048YAP1chr11102027645102027665
ovaryYAP1chr11102028234102028254YAP1chr11102029152102029172
ovaryYAP1chr11102080625102080645chr11102115174102115194
ovaryYAP1chr11102081150102081170chr11102608531102608551
ovaryYAP1chr11102095386102095406chr13113617548113617568
ovaryYAP1chr11102101378102101398chr137942739079427410
ovaryYAP1chr11102102313102102333ATP11Achr13113482670113482690
pancreasYAP1chr11102055972102055992chr145923846559238485
pancreasYAP1chr11102064752102064772YAP1chr11102081228102081248
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 YAP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ370439METAP1D83482172935671172944922YAP134243311102020541102020632

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 # sample11 2    2 2 113 2
GAIN (# sample) 1 2    2 2  12 2
LOSS (# sample)1           1 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr11:101984916-101984916p.Q121Q2
chr11:102076658-102076658p.V241V2
chr11:102100566-102100566p.L416L2
chr11:102094446-102094446p.T322A2
chr11:101985058-101985058p.D169N2
chr11:102100555-102100555p.G413*1
chr11:102033289-102033289p.M225I1
chr11:102100563-102100563p.E415E1
chr11:102100564-102100564p.L416M1
chr11:101984924-101984924p.R124Q1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 5   121 2212 11 4
# mutation21 4   122 2212 11 4
nonsynonymous SNV11 4   1 2  211 11 4
synonymous SNV1  1    2  2  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
chr11:101984916p.Q121Q,YAP12
chr11:102100570p.Q306K,YAP11
chr11:102056845p.E346D,YAP11
chr11:102100588p.T348A,YAP11
chr11:102076776p.R124Q,YAP11
chr11:102100657p.P363Q,YAP11
chr11:101984924p.H126R,YAP11
chr11:102080261p.E419E,YAP11
chr11:102100666p.P129S,YAP11
chr11:101984930p.L420L,YAP11

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 YAP1 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 YAP1

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

ANO6,BICC1,BIRC2,CBL,CUL5,CWF19L2,DIXDC1,
LATS2,LUZP1,MAML2,KMT2A,NPAT,PAFAH1B2,PTPN14,
QKI,RBM7,RDX,SOCS5,TBCEL,USP28,YAP1
CDC14B,DCBLD2,DIXDC1,EXOC6B,FAM160B1,FAM20B,FMNL2,
HEATR5A,LEPROT,MAN1A2,NAB1,PBRM1,PLEKHM3,PTPN21,
SMEK2,SOS1,TLR3,USP33,UTRN,YAP1,ZHX1

BIRC2,C11orf70,FAM217B,CCDC82,COL9A3,GLS,JRKL,
MAML2,MMP27,MMP8,NFAT5,NKD1,OSGIN2,PHF20,
PPP1R2,PPP1R2P3,PTK7,SNTB1,TMEM123,TMEM55A,YAP1
BBX,COL12A1,DIXDC1,DPYSL3,FAM127C,FBXL7,JAM3,
JMY,LOXL4,MID2,PBX1,PCDHGB7,PDE2A,RBFOX2,
RHOJ,SLC16A2,SLIT2,SMARCA1,TMEM43,TMEM47,YAP1
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 YAP1


There's no related Drug.
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Cross referenced IDs for YAP1
* 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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