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 EIF3A
Basic gene info.Gene symbolEIF3A
Gene nameeukaryotic translation initiation factor 3, subunit A
SynonymsEIF3|EIF3S10|P167|TIF32|eIF3-p170|eIF3-theta|p180|p185
CytomapUCSC genome browser: 10q26
Genomic locationchr10 :120794540-120840334
Type of geneprotein-coding
RefGenesNM_003750.2,
Ensembl idENSG00000107581
DescriptionEIF3, p180 subunitcentrosomin homologcytoplasmic protein p167eIF-3-thetaeIF3 p167eIF3 p180eIF3 p185eukaryotic translation initiation factor 3 subunit 10eukaryotic translation initiation factor 3 subunit Aeukaryotic translation initiation factor 3
Modification date20141207
dbXrefs MIM : 602039
HGNC : HGNC
Ensembl : ENSG00000107581
HPRD : 03618
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3A
BioGPS: 8661
Gene Expression Atlas: ENSG00000107581
The Human Protein Atlas: ENSG00000107581
PathwayNCI Pathway Interaction Database: EIF3A
KEGG: EIF3A
REACTOME: EIF3A
ConsensusPathDB
Pathway Commons: EIF3A
MetabolismMetaCyc: EIF3A
HUMANCyc: EIF3A
RegulationEnsembl's Regulation: ENSG00000107581
miRBase: chr10 :120,794,540-120,840,334
TargetScan: NM_003750
cisRED: ENSG00000107581
ContextiHOP: EIF3A
cancer metabolism search in PubMed: EIF3A
UCL Cancer Institute: EIF3A
Assigned class in ccmGDBC

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Phenotypic Information for EIF3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3A
Familial Cancer Database: EIF3A
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EIF3A
MedGen: EIF3A (Human Medical Genetics with Condition)
ClinVar: EIF3A
PhenotypeMGI: EIF3A (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3A

Mutations for EIF3A
* 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
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEIF3Achr10120806586120806606NANOS1chr10120791396120791416
ovaryEIF3Achr10120806586120806606NANOS1chr10120791397120791417
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 EIF3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC014625EIF3A9107110120801629120810165CSF1R106712895149474470149474693
BE797876EIF3A1710810120801969120802060SMARCC110488834763226747680270
DA942713PSMD6128136400805064009080EIF3A27358210120802239120809487
AW501580STAG28135X123202478123205097EIF3A13150210120820815120829131
BF752470EIF3A146410120809314120816354LRRFIP14555872238671873238672005
BM771430EIF3A519210120840140120840327SFXN419261510120900729120914690
AI207430EIF3A137210120801566120801937SLCO1B1362658122129436621294662
BE841770ATP2C218217168443211584438833EIF3A21555610120817711120819163
BE706163OOEP2620367408285974083034EIF3A20138910120810761120816367

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=114)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=4)
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
chr10:120796639-120796639p.R1304H4
chr10:120801850-120801850p.R1061H3
chr10:120810137-120810137p.R790Q2
chr10:120801712-120801712p.R1107Q2
chr10:120825029-120825029p.R335H2
chr10:120832428-120832428p.R172H2
chr10:120795718-120795718p.R1328C2
chr10:120796727-120796727p.R1275S2
chr10:120796733-120796733p.R1273C2
chr10:120816517-120816517p.A671A2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample52 201 4 4  99   512116
# mutation52 251 5 5  1310   1013126
nonsynonymous SNV52 21  5 4  115   811120
synonymous SNV   41   1  25   22 6
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
chr10:120832428p.D953D2
chr10:120802173p.R946T2
chr10:120802195p.R172H2
chr10:120795718p.R1107Q2
chr10:120801850p.R1382H2
chr10:120802033p.R1000Q2
chr10:120801712p.R1061H2
chr10:120795555p.R1328S2
chr10:120801576p.R1061C1
chr10:120802159p.R959Q1

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 EIF3A 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 EIF3A

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

CCDC186,MCMBP,C10orf12,GPATCH11,DDX21,DHX9,EIF3A,
FAM45B,GTF2A1,IDE,LMTK2,NHLRC2,PDZD8,REST,
RIF1,SEC23IP,SLK,SMC3,SPEN,TGFBRAP1,YLPM1
BAZ1B,CAMSAP1,DDX42,EIF3A,ST13P4,FAM168B,GART,
GATC,HDLBP,CLUH,KPNB1,LARP1,MFSD9,NUDT16,
PTPRF,RNASEH1,STAT5B,THRAP3,TNPO3,TXLNG,ZBED3

ABLIM1,ANKRD17,BMS1,EIF3A,GBF1,GOLGA4,INO80,
LARP1,MKI67,NSD1,PDCD11,POLR3A,PPRC1,SEC23IP,
SLK,SLTM,SMC3,THRAP3,YLPM1,ZNF37A,ZNF770
ALMS1,BMS1,BPTF,CDK12,EIF3A,EP400,GCN1L1,
HECTD1,HUWE1,LARP1,LRBA,MDN1,MED1,NUP214,
PRKDC,RANBP2,RIF1,RRP1B,TRRAP,VPRBP,YLPM1
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 EIF3A
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 3, subunit Aapproved; investigationalSirolimus


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Cross referenced IDs for EIF3A
* 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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