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 YAP1

Basic gene info.	Gene symbol	YAP1
	Gene name	Yes-associated protein 1
	Synonyms	COB1\|YAP\|YAP2\|YAP65\|YKI
	Cytomap	UCSC genome browser: 11q13
	Genomic location	chr11 :101981191-102104154
	Type of gene	protein-coding
	RefGenes	NM_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 id	ENSG00000137693
	Description	65 kDa Yes-associated proteinprotein yorkie homologtranscriptional coactivator YAP1yes-associated protein 2yes-associated protein YAP65 homologyorkie homolog
	Modification date	20141222
dbXrefs	MIM : 606608
	HGNC : HGNC
	Ensembl : ENSG00000137693
	HPRD : 09424
	Vega : OTTHUMG00000167322
Protein	UniProt: P46937 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_YAP1
	BioGPS: 10413
	Gene Expression Atlas: ENSG00000137693
	The Human Protein Atlas: ENSG00000137693
Pathway	NCI Pathway Interaction Database: YAP1
	KEGG: YAP1
	REACTOME: YAP1
	ConsensusPathDB
	Pathway Commons: YAP1
Metabolism	MetaCyc: YAP1
	HUMANCyc: YAP1
Regulation	Ensembl's Regulation: ENSG00000137693
	miRBase: chr11 :101,981,191-102,104,154
	TargetScan: NM_001130145
	cisRED: ENSG00000137693
Context	iHOP: YAP1
	cancer metabolism search in PubMed: YAP1
	UCL Cancer Institute: YAP1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of YAP1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: YAP1
	MedGen: YAP1 (Human Medical Genetics with Condition)
	ClinVar: YAP1
Phenotype	MGI: YAP1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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	YAP1	chr11	102014722	102014742	YAP1	chr11	102015522	102015542
ovary	YAP1	chr11	102027028	102027048	YAP1	chr11	102027645	102027665
ovary	YAP1	chr11	102028234	102028254	YAP1	chr11	102029152	102029172
ovary	YAP1	chr11	102080625	102080645		chr11	102115174	102115194
ovary	YAP1	chr11	102081150	102081170		chr11	102608531	102608551
ovary	YAP1	chr11	102095386	102095406		chr13	113617548	113617568
ovary	YAP1	chr11	102101378	102101398		chr13	79427390	79427410
ovary	YAP1	chr11	102102313	102102333	ATP11A	chr13	113482670	113482690
pancreas	YAP1	chr11	102055972	102055992		chr14	59238465	59238485
pancreas	YAP1	chr11	102064752	102064772	YAP1	chr11	102081228	102081248

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 YAP1 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

BQ370439

METAP1D

348

172935671

172944922

YAP1

342

433

102020541

102020632

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	1	1		2					2		2		1	1	3		2
GAIN (# sample)		1		2					2		2			1	2		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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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=3

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Somatic 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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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
chr11:101984916-101984916	p.Q121Q	2
chr11:102076658-102076658	p.V241V	2
chr11:102100566-102100566	p.L416L	2
chr11:102094446-102094446	p.T322A	2
chr11:101985058-101985058	p.D169N	2
chr11:102098268-102098268	p.R357Q	1
chr11:102033193-102033193	p.I193I	1
chr11:102100489-102100489	p.L391I	1
chr11:102033211-102033211	p.W199*	1
chr11:102100555-102100555	p.G413*	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=1

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		5				1	2	1		2	2	1	2		1	1		4
# mutation	2	1		4				1	2	2		2	2	1	2		1	1		4
nonsynonymous SNV	1	1		4				1		2			2	1	1		1	1		4
synonymous SNV	1			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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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
chr11:101984916	p.Q121Q,YAP1	2
chr11:102100563	p.L451F,YAP1	1
chr11:102056767	p.T213T,YAP1	1
chr11:102100566	p.L454I,YAP1	1
chr11:102056830	p.Q221Q,YAP1	1
chr11:102100570	p.L454S,YAP1	1
chr11:102056845	p.W236L,YAP1	1
chr11:102100588	p.S257F,YAP1	1
chr11:102076776	p.R262M,YAP1	1
chr11:102100657	p.R281W,YAP1	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 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

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


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

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 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