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 EIF4A1
Basic gene info.Gene symbolEIF4A1
Gene nameeukaryotic translation initiation factor 4A1
SynonymsDDX2A|EIF-4A|EIF4A|eIF-4A-I|eIF4A-I
CytomapUCSC genome browser: 17p13
Genomic locationchr17 :7476023-7482324
Type of geneprotein-coding
RefGenesNM_001204510.1,
NM_001416.3,
Ensembl idENSG00000161960
DescriptionATP-dependent RNA helicase eIF4A-1eukaryotic initiation factor 4A-Ieukaryotic initiation factor 4AIeukaryotic translation initiation factor 4A
Modification date20141207
dbXrefs MIM : 602641
HGNC : HGNC
Ensembl : ENSG00000161960
HPRD : 04030
Vega : OTTHUMG00000108149
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4A1
BioGPS: 1973
Gene Expression Atlas: ENSG00000161960
The Human Protein Atlas: ENSG00000161960
PathwayNCI Pathway Interaction Database: EIF4A1
KEGG: EIF4A1
REACTOME: EIF4A1
ConsensusPathDB
Pathway Commons: EIF4A1
MetabolismMetaCyc: EIF4A1
HUMANCyc: EIF4A1
RegulationEnsembl's Regulation: ENSG00000161960
miRBase: chr17 :7,476,023-7,482,324
TargetScan: NM_001204510
cisRED: ENSG00000161960
ContextiHOP: EIF4A1
cancer metabolism search in PubMed: EIF4A1
UCL Cancer Institute: EIF4A1
Assigned class in ccmGDBC

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Phenotypic Information for EIF4A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4A1
Familial Cancer Database: EIF4A1
* 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
Orphanet
DiseaseKEGG Disease: EIF4A1
MedGen: EIF4A1 (Human Medical Genetics with Condition)
ClinVar: EIF4A1
PhenotypeMGI: EIF4A1 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF4A1

Mutations for EIF4A1
* 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 EIF4A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN430498FAM120A124299627837996289505EIF4A12383001774821627482224
BC006380NRF1214097129351313129367207EIF4A140715741774784367482036
BQ670981CTSL1155699034357490346046EIF4A15518401774818767482163
CB119692TRAF7402481622278382228046EIF4A12464161774820087482179
AI371755EIF4A113301774817027482031HSPA2325384146500916365009222
CD049225RPL37A10882217366106217366184EIF4A1898891774776057480964
AU119214EIF4A112911774803377480805EIF4A12927881774761447478035

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)                 
LOSS (# sample) 1               
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr17:7476179-7476179p.S7F4
chr17:7480906-7480906p.L263R2
chr17:7480414-7480414p.D185D2
chr17:7476181-7476181p.R8*2
chr17:7477965-7477965p.I58I2
chr17:7480012-7480012p.?2
chr17:7476160-7476160p.M1V1
chr17:7478537-7478537p.Q102Q1
chr17:7481226-7481226p.D330H1
chr17:7480385-7480385p.I176V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1 3 1 1    243  1316
# mutation1 3 1 1    253  1316
nonsynonymous SNV1 1 1 1    251  11 4
synonymous SNV  2          2   212
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
chr17:7476160p.M1I,EIF4A11
chr17:7480480p.K291N,EIF4A11
chr17:7481488p.S7F,EIF4A11
chr17:7476162p.H293D,EIF4A11
chr17:7480687p.S56C,EIF4A11
chr17:7481533p.H303Y,EIF4A11
chr17:7476179p.I58I,EIF4A11
chr17:7480777p.M315I,EIF4A11
chr17:7481668p.G69G,EIF4A11
chr17:7477958p.L332L,EIF4A11

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 EIF4A1 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 EIF4A1

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

AURKB,C1QBP,CTDNEP1,EIF4A1,EIF5A,EIF5AL1,ELAC2,
FXR2,MYBBP1A,NUP88,OVCA2,PELP1,PFN1,PSMB6,
RNMTL1,RPL26,SCO1,SENP3,SLC25A11,TIMM22,WRAP53
APEX1,BYSL,CCT3,DDOST,EIF4A1,ERGIC3,ILF2,
METTL1,MRTO4,NHP2,NME1,NOP16,NPM3,PES1,
POLR1C,PPIA,PRELID1,RAN,RPL7A,RUVBL1,SNRPD1

ATPAF2,ELP5,C1QBP,COPS3,EIF4A1,EIF5A,EIF5AL1,
ELAC2,GEMIN4,MED11,MPDU1,PFN1,PRPSAP2,PSMB6,
RNMTL1,SCO1,SLC25A11,TIMM22,TSR1,WRAP53,YWHAE
HYPK,C19orf10,CCT2,EMC8,EBNA1BP2,EIF3I,EIF4A1,
EIF5AL1,H2AFZ,HNRNPF,NME1,NPM3,PDIA6,PPIB,
PSMD14,PYCRL,RAN,RANBP1,RPL26L1,SNRPD1,SRPRB
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 EIF4A1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877eukaryotic translation initiation factor 4A1approved; investigationalSirolimus
DB01033eukaryotic translation initiation factor 4A1approvedMercaptopurine
DB00563eukaryotic translation initiation factor 4A1approvedMethotrexate


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Cross referenced IDs for EIF4A1
* 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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