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 EIF4A3
Basic gene info.Gene symbolEIF4A3
Gene nameeukaryotic translation initiation factor 4A3
SynonymsDDX48|MUK34|NMP265|NUK34|RCPS|eIF4AIII
CytomapUCSC genome browser: 17q25.3
Genomic locationchr17 :78109012-78120982
Type of geneprotein-coding
RefGenesNM_014740.3,
Ensembl idENSG00000141543
DescriptionATP-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 date20141207
dbXrefs MIM : 608546
HGNC : HGNC
Ensembl : ENSG00000141543
HPRD : 06482
Vega : OTTHUMG00000177538
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4A3
BioGPS: 9775
Gene Expression Atlas: ENSG00000141543
The Human Protein Atlas: ENSG00000141543
PathwayNCI Pathway Interaction Database: EIF4A3
KEGG: EIF4A3
REACTOME: EIF4A3
ConsensusPathDB
Pathway Commons: EIF4A3
MetabolismMetaCyc: EIF4A3
HUMANCyc: EIF4A3
RegulationEnsembl's Regulation: ENSG00000141543
miRBase: chr17 :78,109,012-78,120,982
TargetScan: NM_014740
cisRED: ENSG00000141543
ContextiHOP: EIF4A3
cancer metabolism search in PubMed: EIF4A3
UCL Cancer Institute: EIF4A3
Assigned class in ccmGDBC

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Phenotypic Information for EIF4A3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4A3
Familial Cancer Database: EIF4A3
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EIF4A3
MedGen: EIF4A3 (Human Medical Genetics with Condition)
ClinVar: EIF4A3
PhenotypeMGI: 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.

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 EIF4A3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CR997446RAP1A1721112162464112162535EIF4A371607177811386578120850

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

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr17:78109870-78109870p.D384D2
chr17:78118038-78118038p.E59Q2
chr17:78113891-78113891p.I141L2
chr17:78112043-78112043p.F255F2
chr17:78112849-78112849p.M233I1
chr17:78115160-78115160p.L110F1
chr17:78110120-78110120p.S333C1
chr17:78120709-78120709p.L18F1
chr17:78112879-78112879p.H223H1
chr17:78109893-78109893p.A377P1

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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
# sample55 5  1 21   2  31 5
# mutation65 5  1 21   2  31 5
nonsynonymous SNV55    1 1    2  21 2
synonymous SNV1  5    11      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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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
chr17:78109893p.A377T2
chr17:78115614p.R387H1
chr17:78112043p.D187N1
chr17:78115630p.H158L1
chr17:78110034p.I362V1
chr17:78112828p.D154H1
chr17:78117975p.L354F1
chr17:78110058p.I141I1
chr17:78112879p.L348L1
chr17:78117984p.D131D1

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 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

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

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
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 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

: Open all cross reference information



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