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 EIF4A2
Basic gene info.Gene symbolEIF4A2
Gene nameeukaryotic translation initiation factor 4A2
SynonymsBM-010|DDX2B|EIF4A|EIF4F|eIF-4A-II|eIF4A-II
CytomapUCSC genome browser: 3q28
Genomic locationchr3 :186501360-186507685
Type of geneprotein-coding
RefGenesNM_001967.3,
Ensembl idENSG00000156976
DescriptionATP-dependent RNA helicase eIF4A-2eukaryotic initiation factor 4A-II
Modification date20141207
dbXrefs MIM : 601102
HGNC : HGNC
Ensembl : ENSG00000156976
HPRD : 03062
Vega : OTTHUMG00000156564
ProteinUniProt: Q14240
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4A2
BioGPS: 1974
Gene Expression Atlas: ENSG00000156976
The Human Protein Atlas: ENSG00000156976
PathwayNCI Pathway Interaction Database: EIF4A2
KEGG: EIF4A2
REACTOME: EIF4A2
ConsensusPathDB
Pathway Commons: EIF4A2
MetabolismMetaCyc: EIF4A2
HUMANCyc: EIF4A2
RegulationEnsembl's Regulation: ENSG00000156976
miRBase: chr3 :186,501,360-186,507,685
TargetScan: NM_001967
cisRED: ENSG00000156976
ContextiHOP: EIF4A2
cancer metabolism search in PubMed: EIF4A2
UCL Cancer Institute: EIF4A2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF4A2 in cancer cell metabolism1. Yan LX, Wu QN, Zhang Y, Li YY, Liao DZ, et al. (2011) Knockdown of miR-21 in human breast cancer cell lines inhibits proliferation, in vitro migration and in vivo tumor growth. Breast Cancer Res 13: R2. doi: 10.1186/bcr2803. pmid: 3109565. go to article
2. Shaoyan X, Juanjuan Y, Yalan T, Ping H, Jianzhong L, et al. (2013) Downregulation of EIF4A2 in non-small-cell lung cancer associates with poor prognosis. Clin Lung Cancer 14: 658-665. doi: 10.1016/j.cllc.2013.04.011. go to article

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Phenotypic Information for EIF4A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4A2
Familial Cancer Database: EIF4A2
* 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_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 601102; gene.
Orphanet
DiseaseKEGG Disease: EIF4A2
MedGen: EIF4A2 (Human Medical Genetics with Condition)
ClinVar: EIF4A2
PhenotypeMGI: EIF4A2 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF4A2

Mutations for EIF4A2
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 EIF4A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF990739DLG514119107957970779584177EIF4A21192953186502123186502299
DA558800EIF4A21683186505472186505539LMNA695491156084526156085006
BM773122EIF4A2204153186504914186506183FUS410506163120278431202880
BM781579EIF4A2204143186504914186506183FUS409551163120278431202926
AW840050EIF4A262973186505669186505963EIF4A22923423186505654186505704
BG979271EIF4A293113186506486186506792EIF4A23053773186506836186506908
BQ355782KIAA121713186102483313924833314EIF4A21764503186507348186507622
AI810008ATP6V1C2714821092351710923658EIF4A21415433186506429186506831
DA027118EIF4A214633186501366186503752TGFBI4645575135364680135364773
BM834299EIF4A21693186501368186501436PPDPF65562206215336562153862
BF840289ACTR27731326549728665497523EIF4A23125013186506064186506253
BF987336DLG514119107957970779584177EIF4A21192953186502123186502299

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 # sample          1      
GAIN (# sample)          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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
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
chr3:186503976-186503976p.V181L3
chr3:186506990-186506990p.R386G2
chr3:186504345-186504345p.F228I2
chr3:186503977-186503977p.V181A2
chr3:186504030-186504030p.E199K2
chr3:186503788-186503788p.I155I1
chr3:186505350-186505350p.V326F1
chr3:186501401-186501401p.M1K1
chr3:186504304-186504304p.S214C1
chr3:186502455-186502455p.Q60*1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 12  1 3  532  54 6
# mutation14 8  1 3  532  54 7
nonsynonymous SNV14 7    3  422  24 6
synonymous SNV   1  1    11   3  1
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
chr3:186506990p.R386S3
chr3:186503977p.N356T2
chr3:186505659p.V181A2
chr3:186504980p.S5F1
chr3:186501407p.I233L1
chr3:186505363p.G336W1
chr3:186503976p.I24I1
chr3:186504984p.F250C1
chr3:186501413p.G336E1
chr3:186505598p.E25Q1

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 EIF4A2 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 EIF4A2

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

BCL2,EFCAB7,EIF2A,EIF4A2,FXR1,MBLAC2,MED13L,
MYEF2,PHF21A,RABGGTB,SCAPER,SENP2,SLC25A36,THAP2,
TYW3,VPS8,ZSCAN26,ZNF24,ZNF33B,ZRANB2,ZSWIM6
ABCB7,ATAD1,FOPNL,TRMT1L,CCNG1,CNOT4,COPS2,
CRBN,DCTN4,DYM,EIF4A2,EIF4B,FAM175A,GIN1,
POLR2M___GCOM1,LIAS,LRPPRC,PHF10,RCOR3,TRIM23,ZRANB1

ZFAS1,C3orf17,EEF1B2,EIF2A,EIF4A2,MYNN,NMD3,
RPL10A,RPL12,RPL15,RPL24,RPL32,RPL35A,RPL7A,
RPS11,RPS15A,RPS18,RPS3A,RYK,SERP1,SLC25A36
AMZ2P1,ARL3,BBS10,BEX4,CAMLG,COMMD6,EIF4A2,
FAM175A,IFT46,LZTFL1,MEAF6,PCMTD1,RRAGB,RYK,
SNRPN,SPATA7,TCEAL1,TCEAL8,UBE2Q2,ZSCAN26,ZNF691
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 EIF4A2


There's no related Drug.
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Cross referenced IDs for EIF4A2
* 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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