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 TEAD2
Basic gene info.Gene symbolTEAD2
Gene nameTEA domain family member 2
SynonymsETF|TEAD-2|TEF-4|TEF4
CytomapUCSC genome browser: 19q13.3
Genomic locationchr19 :49843852-49865714
Type of geneprotein-coding
RefGenesNM_001256658.1,
NM_001256659.1,NM_001256660.1,NM_001256661.1,NM_001256662.1,
NM_003598.1,
Ensembl idENSG00000074219
Descriptiontranscriptional enhancer factor TEF-4
Modification date20141207
dbXrefs MIM : 601729
HGNC : HGNC
Ensembl : ENSG00000074219
Vega : OTTHUMG00000183174
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TEAD2
BioGPS: 8463
Gene Expression Atlas: ENSG00000074219
The Human Protein Atlas: ENSG00000074219
PathwayNCI Pathway Interaction Database: TEAD2
KEGG: TEAD2
REACTOME: TEAD2
ConsensusPathDB
Pathway Commons: TEAD2
MetabolismMetaCyc: TEAD2
HUMANCyc: TEAD2
RegulationEnsembl's Regulation: ENSG00000074219
miRBase: chr19 :49,843,852-49,865,714
TargetScan: NM_001256658
cisRED: ENSG00000074219
ContextiHOP: TEAD2
cancer metabolism search in PubMed: TEAD2
UCL Cancer Institute: TEAD2
Assigned class in ccmGDBC

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Phenotypic Information for TEAD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TEAD2
MedGen: TEAD2 (Human Medical Genetics with Condition)
ClinVar: TEAD2
PhenotypeMGI: TEAD2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TEAD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP394212TEAD21127194984431049844436PPY128331174201817342018566
BG983176PHLDB1114311118498068118498210TEAD2129586194984595149846684

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 # sample21               
GAIN (# sample)21               
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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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=4

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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=12)
Stat. for Deletions
(# total SNVs=24)
Stat. for Insertions
(# total SNVs=3)

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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
chr19:49850473-49850473p.H295fs*1218
chr19:49850472-49850473p.H295fs*193
chr19:49862705-49862705p.R95Q3
chr19:49858607-49858608p.P144fs*153
chr19:49845767-49845767p.F386F2
chr19:49850484-49850484p.R291H2
chr19:49860531-49860531p.R113K2
chr19:49852054-49852054p.S214W2
chr19:49862699-49862699p.R97Q2
chr19:49862706-49862706p.R95R2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31152 1 1  463  49 11
# mutation31162 1 1  563  59 11
nonsynonymous SNV21151   1  142  45 9
synonymous SNV1  11 1    421  14 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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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
chr19:49862705p.R95Q,TEAD23
chr19:49862699p.V303V,TEAD22
chr19:49850456p.R97Q,TEAD22
chr19:49858608p.A143A,TEAD21
chr19:49863137p.G29D,TEAD21
chr19:49846506p.P313S,TEAD21
chr19:49850485p.S136S,TEAD21
chr19:49858629p.G29S,TEAD21
chr19:49863201p.D308V,TEAD21
chr19:49846519p.I115I,TEAD21

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 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

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.

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

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
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 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



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