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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TEAD4 |
Basic gene info. | Gene symbol | TEAD4 |
Gene name | TEA domain family member 4 | |
Synonyms | EFTR-2|RTEF1|TCF13L1|TEF-3|TEF3|TEFR-1|hRTEF-1B | |
Cytomap | UCSC genome browser: 12p13.3-p13.2 | |
Genomic location | chr12 :3068477-3149842 | |
Type of gene | protein-coding | |
RefGenes | NM_003213.3, NM_201441.2,NM_201443.2, | |
Ensembl id | ENSG00000197905 | |
Description | related transcription enhancer factor 1Btranscription factor 13-like 1transcription factor RTEF-1transcriptional enhancer factor 1-relatedtranscriptional enhancer factor 3transcriptional enhancer factor TEF-3 | |
Modification date | 20141207 | |
dbXrefs | MIM : 601714 | |
HGNC : HGNC | ||
Ensembl : ENSG00000197905 | ||
HPRD : 03421 | ||
Vega : OTTHUMG00000168153 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TEAD4 | |
BioGPS: 7004 | ||
Gene Expression Atlas: ENSG00000197905 | ||
The Human Protein Atlas: ENSG00000197905 | ||
Pathway | NCI Pathway Interaction Database: TEAD4 | |
KEGG: TEAD4 | ||
REACTOME: TEAD4 | ||
ConsensusPathDB | ||
Pathway Commons: TEAD4 | ||
Metabolism | MetaCyc: TEAD4 | |
HUMANCyc: TEAD4 | ||
Regulation | Ensembl's Regulation: ENSG00000197905 | |
miRBase: chr12 :3,068,477-3,149,842 | ||
TargetScan: NM_003213 | ||
cisRED: ENSG00000197905 | ||
Context | iHOP: TEAD4 | |
cancer metabolism search in PubMed: TEAD4 | ||
UCL Cancer Institute: TEAD4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for TEAD4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TEAD4 |
Familial Cancer Database: TEAD4 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: TEAD4 |
MedGen: TEAD4 (Human Medical Genetics with Condition) | |
ClinVar: TEAD4 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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 | TEAD4 | chr12 | 3111233 | 3111253 | TEAD4 | chr12 | 3111293 | 3111313 |
ovary | TEAD4 | chr12 | 3123720 | 3123740 | TEAD4 | chr12 | 3121440 | 3121460 |
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 TEAD4 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 |
AI952989 | C15orf39 | 1 | 371 | 15 | 75504138 | 75504508 | TEAD4 | 370 | 499 | 12 | 3149778 | 3149907 | |
BE731603 | TEAD4 | 1 | 78 | 12 | 3103911 | 3104429 | TEAD4 | 70 | 704 | 12 | 3103970 | 3129895 |
Other DBs for Structural Variants |
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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 |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=37) | (# total SNVs=11) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr12:3131110-3131110 | p.P275L | 2 |
chr12:3104142-3104142 | p.D70D | 2 |
chr12:3131142-3131142 | p.E286K | 2 |
chr12:3104002-3104002 | p.A24T | 2 |
chr12:3147152-3147152 | p.I306F | 2 |
chr12:3129850-3129850 | p.P212S | 2 |
chr12:3149557-3149557 | p.E406E | 2 |
chr12:3128346-3128346 | p.? | 2 |
chr12:3126691-3126691 | p.G161V | 1 |
chr12:3129815-3129825 | p.G201fs*68 | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 3 | 1 |   | 1 |   |   |   |   | 8 |   |   |   |   | 9 | 8 | 1 | 15 |
# mutation | 2 | 1 |   | 3 | 1 |   | 1 |   |   |   |   | 8 |   |   |   |   | 9 | 8 | 1 | 16 |
nonsynonymous SNV | 2 | 1 |   | 3 |   |   | 1 |   |   |   |   | 7 |   |   |   |   | 7 | 5 | 1 | 9 |
synonymous SNV |   |   |   |   | 1 |   |   |   |   |   |   | 1 |   |   |   |   | 2 | 3 |   | 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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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 |
chr12:3131141 | p.D70D,TEAD4 | 2 |
chr12:3131142 | p.F156F,TEAD4 | 2 |
chr12:3104142 | p.E157K,TEAD4 | 2 |
chr12:3128321 | p.R111C,TEAD4 | 1 |
chr12:3129908 | p.P83S,TEAD4 | 1 |
chr12:3120173 | p.P194P,TEAD4 | 1 |
chr12:3128322 | p.R111R,TEAD4 | 1 |
chr12:3129912 | p.P84L,TEAD4 | 1 |
chr12:3120219 | p.T200A,TEAD4 | 1 |
chr12:3128323 | p.S5L,TEAD4 | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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