Cancer Cell Metabolism Gene Database

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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 EIF3E
Basic gene info.Gene symbolEIF3E
Gene nameeukaryotic translation initiation factor 3, subunit E
SynonymsEIF3-P48|EIF3S6|INT6|eIF3-p46
CytomapUCSC genome browser: 8q22-q23
Genomic locationchr8 :109213971-109260959
Type of geneprotein-coding
RefGenesNM_001568.2,
Ensembl idENSG00000104408
DescriptioneIF-3 p48eukaryotic translation initiation factor 3 subunit 6eukaryotic translation initiation factor 3 subunit Eeukaryotic translation initiation factor 3, subunit 6 (48kD)eukaryotic translation initiation factor 3, subunit 6 48kDamammary tumor-asso
Modification date20141222
dbXrefs MIM : 602210
HGNC : HGNC
Ensembl : ENSG00000104408
HPRD : 03734
Vega : OTTHUMG00000164858
ProteinUniProt: P60228
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3E
BioGPS: 3646
Gene Expression Atlas: ENSG00000104408
The Human Protein Atlas: ENSG00000104408
PathwayNCI Pathway Interaction Database: EIF3E
KEGG: EIF3E
REACTOME: EIF3E
ConsensusPathDB
Pathway Commons: EIF3E
MetabolismMetaCyc: EIF3E
HUMANCyc: EIF3E
RegulationEnsembl's Regulation: ENSG00000104408
miRBase: chr8 :109,213,971-109,260,959
TargetScan: NM_001568
cisRED: ENSG00000104408
ContextiHOP: EIF3E
cancer metabolism search in PubMed: EIF3E
UCL Cancer Institute: EIF3E
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF3E in cancer cell metabolism1. Cen B, Xiong Y, Song JH, Mahajan S, DuPont R, et al. (2014) The Pim-1 protein kinase is an important regulator of MET receptor tyrosine kinase levels and signaling. Mol Cell Biol 34: 2517-2532. doi: 10.1128/MCB.00147-14. pmid: 4054323. go to article
2. Martineau Y, Wang X, Alain T, Petroulakis E, Shahbazian D, et al. (2014) Control of Paip1-eukayrotic translation initiation factor 3 interaction by amino acids through S6 kinase. Mol Cell Biol 34: 1046-1053. doi: 10.1128/MCB.01079-13. pmid: 3958023. go to article
3. Yuan Y, Zhang Y, Yao S, Shi H, Huang X, et al. (2014) The translation initiation factor eIF3i up-regulates vascular endothelial growth factor A, accelerates cell proliferation, and promotes angiogenesis in embryonic development and tumorigenesis. J Biol Chem 289: 28310-28323. doi: 10.1074/jbc.M114.571356. pmid: 4192485. go to article

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Phenotypic Information for EIF3E(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3E
Familial Cancer Database: EIF3E
* 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 602210; gene.
Orphanet
DiseaseKEGG Disease: EIF3E
MedGen: EIF3E (Human Medical Genetics with Condition)
ClinVar: EIF3E
PhenotypeMGI: EIF3E (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3E

Mutations for EIF3E
* 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
* 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
ovaryEIF3Echr8109241051109241071EIF3Echr8109241866109241886
ovaryEIF3Echr8109260140109260160chr8109296582109296602
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 EIF3E related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA000478EIF3E11298109254115109260942GTSE1128525224669327546704453
BF799939EIF3E172728109228642109240524PRSS23264662118651929986519699

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 # sample2             1  
GAIN (# sample)1             1  
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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=57)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr8:109240603-109240603p.L205L6
chr8:109240604-109240604p.L205P5
chr8:109215229-109215229p.Q428*3
chr8:109248412-109248412p.D115G2
chr8:109241355-109241355p.N181D2
chr8:109260856-109260856p.L26I2
chr8:109226865-109226865p.F344F2
chr8:109252288-109252288p.R74S2
chr8:109260902-109260902p.I10I2
chr8:109241421-109241421p.P159T2

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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=11

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample233171 2 11 664  22 7
# mutation23381 2 11 674  22 11
nonsynonymous SNV 1261 2 1  464  11 10
synonymous SNV2212     1 21   11 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
chr8:109240603p.L205L6
chr8:109240604p.L205P5
chr8:109215282p.I10I2
chr8:109260902p.S410N2
chr8:109226922p.N429I1
chr8:109254056p.F305F1
chr8:109240540p.W182L1
chr8:109241378p.A11A1
chr8:109226942p.N421H1
chr8:109254087p.V280F1

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 EIF3E 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 EIF3E

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

C8orf59,CHMP4C,DCAF13,EIF3E,ENY2,LOC442454,MRPL15,
MTERF3,NUDCD1,PABPC1,PABPC3,PTDSS1,RPL30,RPL7,
SLC25A32,TATDN1,EMC2,UBE2V2,UQCRB,WDYHV1,ZFAND1
CCNB1IP1,EIF2A,EIF2S3,EIF3E,EIF3L,EIF3M,LTA4H,
NAP1L1,PABPC1,PMPCB,RPL15,RPL22,RPL7,RPS3A,
RSL1D1,RSL24D1,TAF1D,TATDN1,TIMM9,TOMM20,ZNF277

ANKRD46,AZIN1,NDUFAF6,C8orf59,COPS5,DCAF13,DPY19L4,
E2F5,EBAG9,EIF3E,EIF3H,MED30,MRPL13,NSMCE2,
PABPC1,RPL30,RPL8,TATDN1,EMC2,WDYHV1,ZFAND1
BOD1,BTF3,C11orf57,DPH5,EEF1A1P9,EIF3E,POLR2M___GCOM1,
ICE2,RPL10,RPL10A,RPL14,RPL15,RPL34,RPL5,
RPS15A,RSL1D1,TIMM9,TMEM182,UTP23,ZFAND1,ZNF614
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 EIF3E


There's no related Drug.
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Cross referenced IDs for EIF3E
* 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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