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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for EIF4A3 |
Basic gene info. | Gene symbol | EIF4A3 |
Gene name | eukaryotic translation initiation factor 4A3 | |
Synonyms | DDX48|MUK34|NMP265|NUK34|RCPS|eIF4AIII | |
Cytomap | UCSC genome browser: 17q25.3 | |
Genomic location | chr17 :78109012-78120982 | |
Type of gene | protein-coding | |
RefGenes | NM_014740.3, | |
Ensembl id | ENSG00000141543 | |
Description | ATP-dependent RNA helicase DDX48ATP-dependent RNA helicase eIF4A-3DEAD (Asp-Glu-Ala-Asp) box polypeptide 48DEAD box protein 48NMP 265eIF-4A-IIIeIF4A-IIIeukaryotic initiation factor 4A-IIIeukaryotic initiation factor 4A-like NUK-34eukaryotic trans | |
Modification date | 20141207 | |
dbXrefs | MIM : 608546 | |
HGNC : HGNC | ||
Ensembl : ENSG00000141543 | ||
HPRD : 06482 | ||
Vega : OTTHUMG00000177538 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_EIF4A3 | |
BioGPS: 9775 | ||
Gene Expression Atlas: ENSG00000141543 | ||
The Human Protein Atlas: ENSG00000141543 | ||
Pathway | NCI Pathway Interaction Database: EIF4A3 | |
KEGG: EIF4A3 | ||
REACTOME: EIF4A3 | ||
ConsensusPathDB | ||
Pathway Commons: EIF4A3 | ||
Metabolism | MetaCyc: EIF4A3 | |
HUMANCyc: EIF4A3 | ||
Regulation | Ensembl's Regulation: ENSG00000141543 | |
miRBase: chr17 :78,109,012-78,120,982 | ||
TargetScan: NM_014740 | ||
cisRED: ENSG00000141543 | ||
Context | iHOP: EIF4A3 | |
cancer metabolism search in PubMed: EIF4A3 | ||
UCL Cancer Institute: EIF4A3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for EIF4A3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: EIF4A3 |
Familial Cancer Database: EIF4A3 |
* 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_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: EIF4A3 |
MedGen: EIF4A3 (Human Medical Genetics with Condition) | |
ClinVar: EIF4A3 | |
Phenotype | MGI: EIF4A3 (International Mouse Phenotyping Consortium) |
PhenomicDB: EIF4A3 |
Mutations for EIF4A3 |
* 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 EIF4A3 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 |
CR997446 | RAP1A | 1 | 72 | 1 | 112162464 | 112162535 | EIF4A3 | 71 | 607 | 17 | 78113865 | 78120850 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=23) | (# total SNVs=14) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr17:78118038-78118038 | p.E59Q | 2 |
chr17:78113891-78113891 | p.I141L | 2 |
chr17:78112043-78112043 | p.F255F | 2 |
chr17:78109870-78109870 | p.D384D | 2 |
chr17:78110058-78110058 | p.L354F | 1 |
chr17:78117976-78117976 | p.I79I | 1 |
chr17:78111277-78111277 | p.M297I | 1 |
chr17:78113839-78113839 | p.H158L | 1 |
chr17:78110071-78110071 | p.I349I | 1 |
chr17:78117984-78117984 | p.D77H | 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 | 5 | 5 |   | 5 |   |   | 1 |   | 2 | 1 |   |   |   | 2 |   |   | 3 | 1 |   | 5 |
# mutation | 6 | 5 |   | 5 |   |   | 1 |   | 2 | 1 |   |   |   | 2 |   |   | 3 | 1 |   | 5 |
nonsynonymous SNV | 5 | 5 |   |   |   |   | 1 |   | 1 |   |   |   |   | 2 |   |   | 2 | 1 |   | 2 |
synonymous SNV | 1 |   |   | 5 |   |   |   |   | 1 | 1 |   |   |   |   |   |   | 1 |   |   | 3 |
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 |
chr17:78109893 | p.A377T | 2 |
chr17:78111190 | p.F265C | 1 |
chr17:78113839 | p.E59Q | 1 |
chr17:78120641 | p.E261K | 1 |
chr17:78111203 | p.Y56Y | 1 |
chr17:78113852 | p.F255F | 1 |
chr17:78120703 | p.F40L | 1 |
chr17:78111277 | p.L240L | 1 |
chr17:78113889 | p.E20Q | 1 |
chr17:78120709 | p.H223H | 1 |
Other DBs for Point Mutations |
Copy Number for EIF4A3 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 EIF4A3 |
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 |
ACTG1,ARHGDIA,BIRC5,METTL23,CCDC137,EIF4A3,EPR1, FOXK2,GPS1,JMJD6,MRPL12,MRPS7,NPLOC4,NUP85, RPTOR,SLC25A19,SRP68,STRA13,ALYREF,UBE2O,WDR45B | APH1A,ARFIP2,BAIAP2,C11orf49,CADM4,CHST10,CLDN7, EBNA1BP2,EIF4A3,HNRNPM,KRT18,LOC92659,MFAP1,PHF23, PRKCZ,PRPF19,PRRG2,RAB17,RBM4,SNRNP40,SPINT2 |
BIRC5,EFTUD2,EIF4A3,EPR1,ICT1,LRRC59,MRPL12, MRPL27,MRPL38,MRPS7,NME1,NUP85,PHB,PSMD11, SLC25A19,SRP68,TACO1,ALYREF,TK1,UTP18,WDR45B | C1QBP,CCT5,CHEK2,DBF4,DPH2,EIF4A3,GINS1, GINS2,HEATR3,HNRNPF,INTS7,METTL1,MTFP1,PCNA, PHB,POLE2,RFC2,SNRPB,TMX2,UBE2T,UMPS |
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 EIF4A3 |
There's no related Drug. |
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Cross referenced IDs for EIF4A3 |
* 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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