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 TEAD4
Basic gene info.Gene symbolTEAD4
Gene nameTEA domain family member 4
SynonymsEFTR-2|RTEF1|TCF13L1|TEF-3|TEF3|TEFR-1|hRTEF-1B
CytomapUCSC genome browser: 12p13.3-p13.2
Genomic locationchr12 :3068477-3149842
Type of geneprotein-coding
RefGenesNM_003213.3,
NM_201441.2,NM_201443.2,
Ensembl idENSG00000197905
Descriptionrelated transcription enhancer factor 1Btranscription factor 13-like 1transcription factor RTEF-1transcriptional enhancer factor 1-relatedtranscriptional enhancer factor 3transcriptional enhancer factor TEF-3
Modification date20141207
dbXrefs MIM : 601714
HGNC : HGNC
Ensembl : ENSG00000197905
HPRD : 03421
Vega : OTTHUMG00000168153
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TEAD4
BioGPS: 7004
Gene Expression Atlas: ENSG00000197905
The Human Protein Atlas: ENSG00000197905
PathwayNCI Pathway Interaction Database: TEAD4
KEGG: TEAD4
REACTOME: TEAD4
ConsensusPathDB
Pathway Commons: TEAD4
MetabolismMetaCyc: TEAD4
HUMANCyc: TEAD4
RegulationEnsembl's Regulation: ENSG00000197905
miRBase: chr12 :3,068,477-3,149,842
TargetScan: NM_003213
cisRED: ENSG00000197905
ContextiHOP: TEAD4
cancer metabolism search in PubMed: TEAD4
UCL Cancer Institute: TEAD4
Assigned class in ccmGDBC

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Phenotypic Information for TEAD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TEAD4
Familial Cancer Database: TEAD4
* 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: TEAD4
MedGen: TEAD4 (Human Medical Genetics with Condition)
ClinVar: TEAD4
PhenotypeMGI: TEAD4 (International Mouse Phenotyping Consortium)
PhenomicDB: TEAD4

Mutations for TEAD4
* 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
ovaryTEAD4chr1231112333111253TEAD4chr1231112933111313
ovaryTEAD4chr1231237203123740TEAD4chr1231214403121460
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 TEAD4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI952989C15orf391371157550413875504508TEAD43704991231497783149907
BE731603TEAD41781231039113104429TEAD4707041231039703129895

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 # sample1     2      1   
GAIN (# sample)1     2      1   
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=2

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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=11)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr12:3147152-3147152p.I306F2
chr12:3129850-3129850p.P212S2
chr12:3149557-3149557p.E406E2
chr12:3128346-3128346p.?2
chr12:3131110-3131110p.P275L2
chr12:3104142-3104142p.D70D2
chr12:3131142-3131142p.E286K2
chr12:3104002-3104002p.A24T2
chr12:3121375-3121375p.R111C1
chr12:3131073-3131073p.E263K1

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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
# sample21 31 1    8    98115
# mutation21 31 1    8    98116
nonsynonymous SNV21 3  1    7    7519
synonymous SNV    1      1    23 7
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
chr12:3131141p.E157K,TEAD42
chr12:3131142p.D70D,TEAD42
chr12:3104142p.F156F,TEAD42
chr12:3129854p.P81S,TEAD41
chr12:3131110p.T92T,TEAD41
chr12:3104151p.P81L,TEAD41
chr12:3128321p.K168T,TEAD41
chr12:3129908p.R93S,TEAD41
chr12:3120173p.P83S,TEAD41
chr12:3128322p.P194P,TEAD41

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 TEAD4 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 TEAD4

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

CCDC77,CDC20,CDCA3,YBX3,YBX3P1,DERA,EMG1,
FOXM1,GAPDH,LDHB,MAGOHB,MLF2,MRPL51,NCAPD2,
NDUFA9,NOP2,PHB2,RAD51AP1,TEAD4,TPI1,TULP3
PERM1,CARM1,CCDC28B,CHRNB1,YBX3,DNAJB5,DYRK1B,
FHL3,GAMT,GAPDH,IL32,IPO13,JSRP1,MYL6B,
PTP4A3,RRAD,SCN1B,SH2B2,SHISA4,TEAD4,TPM2

ADIPOR2,B4GALNT3,RHNO1,C12orf5,CCDC77,CHRNA6,DCP1B,
CRACR2A,FBXL14,FKBP4,FOXM1,GPR139,IFNA13,ITFG2,
KRTAP8-1,MIR31HG,NKX6-3,OR9K2,PARP11,TEAD4,TULP3
ANKRD22,CDC7,CYP19A1,FAM57A,GRAMD2,HAUS7,LIPG,
LRP8,MLKL,MMP3,MTHFD1L,MVK,NSDHL,PDIA6,
PPIB,SDF2L1,SLC38A5,STARD4,TEAD4,TSTA3,WDR4
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 TEAD4


There's no related Drug.
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Cross referenced IDs for TEAD4
* 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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