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 TEAD2

Basic gene info.	Gene symbol	TEAD2
	Gene name	TEA domain family member 2
	Synonyms	ETF\|TEAD-2\|TEF-4\|TEF4
	Cytomap	UCSC genome browser: 19q13.3
	Genomic location	chr19 :49843852-49865714
	Type of gene	protein-coding
	RefGenes	NM_001256658.1, NM_001256659.1,NM_001256660.1,NM_001256661.1,NM_001256662.1, NM_003598.1,
	Ensembl id	ENSG00000074219
	Description	transcriptional enhancer factor TEF-4
	Modification date	20141207
dbXrefs	MIM : 601729
	HGNC : HGNC
	Ensembl : ENSG00000074219
	Vega : OTTHUMG00000183174
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TEAD2
	BioGPS: 8463
	Gene Expression Atlas: ENSG00000074219
	The Human Protein Atlas: ENSG00000074219
Pathway	NCI Pathway Interaction Database: TEAD2
	KEGG: TEAD2
	REACTOME: TEAD2
	ConsensusPathDB
	Pathway Commons: TEAD2
Metabolism	MetaCyc: TEAD2
	HUMANCyc: TEAD2
Regulation	Ensembl's Regulation: ENSG00000074219
	miRBase: chr19 :49,843,852-49,865,714
	TargetScan: NM_001256658
	cisRED: ENSG00000074219
Context	iHOP: TEAD2
	cancer metabolism search in PubMed: TEAD2
	UCL Cancer Institute: TEAD2
Assigned class in ccmGDB	C

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Phenotypic Information for TEAD2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TEAD2
	Familial Cancer Database: TEAD2

* 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
Orphanet
Disease	KEGG Disease: TEAD2
	MedGen: TEAD2 (Human Medical Genetics with Condition)
	ClinVar: TEAD2
Phenotype	MGI: TEAD2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TEAD2

Mutations for TEAD2

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TEAD2 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
BP394212	TEAD2	1	127	19	49844310	49844436	PPY	128	331	17	42018173	42018566
BG983176	PHLDB1	1	143	11	118498068	118498210	TEAD2	129	586	19	49845951	49846684

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=4

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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=12)

Stat. for Deletions (# total SNVs=24)	Stat. for Insertions (# total SNVs=3)

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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
chr19:49850473-49850473	p.H295fs*12	18
chr19:49850472-49850473	p.H295fs*19	3
chr19:49862705-49862705	p.R95Q	3
chr19:49858607-49858608	p.P144fs*15	3
chr19:49845767-49845767	p.F386F	2
chr19:49850484-49850484	p.R291H	2
chr19:49860531-49860531	p.R113K	2
chr19:49852054-49852054	p.S214W	2
chr19:49862699-49862699	p.R97Q	2
chr19:49862706-49862706	p.R95R	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=3

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	3	1	1	5	2		1		1			4	6	3			4	9		11
# mutation	3	1	1	6	2		1		1			5	6	3			5	9		11
nonsynonymous SNV	2	1	1	5	1				1			1	4	2			4	5		9
synonymous SNV	1			1	1		1					4	2	1			1	4		2

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
chr19:49862705	p.R95Q,TEAD2	3
chr19:49862699	p.V303V,TEAD2	2
chr19:49850456	p.R97Q,TEAD2	2
chr19:49845839	p.L339L,TEAD2	1
chr19:49863116	p.R224W,TEAD2	1
chr19:49850474	p.P39P,TEAD2	1
chr19:49858608	p.E337K,TEAD2	1
chr19:49846506	p.A220A,TEAD2	1
chr19:49863137	p.G38G,TEAD2	1
chr19:49850485	p.A318V,TEAD2	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 TEAD2 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 TEAD2

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


BCL2L12,DBN1,DKKL1,EFNA4,FAM89B,FBLIM1,FBXO46, GTF2H4,MEX3A,NASP,NCK2,POLD1,PPP1R14B,PRMT1, TCF3,TEAD2,TEAD3,TUBB,UBE2E3,VASP,ZNF71	AGRN,AMPD2,C17orf70,FAM213B,CACNB3,CHPF2,CHPF, EPHB4,FBLIM1,FBXL19,FRMD8,GATAD2A,GPSM1,NSMF, NGFR,PITPNM1,SEPT9,TCF3,TEAD2,TRAF7,VWA1

ZNF503-AS2,NREP,CD46,CNN3,CPA6,DKKL1,ENPP3, GYLTL1B,LGR5,MEX3A,OXGR1,SEMA4C,SETMAR,SH3BP4, SOX4,TEAD2,TET1,THAP2,TLR4,VASH2,ZNF124	BAG2,CCDC69,CETN2,CFL2,FEZ1,MORN5,MXRA7, PEA15,PLEKHO1,PLN,PSD,PTBP2,PTPLA,RAB23, RAB34,RHOQ,SMARCD3,ST3GAL3,TEAD2,TMEM55A,ZNF25

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 TEAD2

There's no related Drug.

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Cross referenced IDs for TEAD2

* 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