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 EIF4G1
Basic gene info.Gene symbolEIF4G1
Gene nameeukaryotic translation initiation factor 4 gamma, 1
SynonymsEIF-4G1|EIF4F|EIF4G|EIF4GI|P220|PARK18
CytomapUCSC genome browser: 3q27.1
Genomic locationchr3 :184032282-184053146
Type of geneprotein-coding
RefGenesNM_001194946.1,
NM_001194947.1,NM_001291157.1,NM_004953.4,NM_182917.4,
NM_198241.2,NM_198242.2,NM_198244.2,
Ensembl idENSG00000114867
DescriptionEIF4-gammaeIF-4-gamma 1eucaryotic translation initiation factor 4Geukaryotic translation initiation factor 4 gamma 1
Modification date20141207
dbXrefs MIM : 600495
HGNC : HGNC
Ensembl : ENSG00000114867
HPRD : 06774
Vega : OTTHUMG00000156784
ProteinUniProt: Q04637
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4G1
BioGPS: 1981
Gene Expression Atlas: ENSG00000114867
The Human Protein Atlas: ENSG00000114867
PathwayNCI Pathway Interaction Database: EIF4G1
KEGG: EIF4G1
REACTOME: EIF4G1
ConsensusPathDB
Pathway Commons: EIF4G1
MetabolismMetaCyc: EIF4G1
HUMANCyc: EIF4G1
RegulationEnsembl's Regulation: ENSG00000114867
miRBase: chr3 :184,032,282-184,053,146
TargetScan: NM_001194946
cisRED: ENSG00000114867
ContextiHOP: EIF4G1
cancer metabolism search in PubMed: EIF4G1
UCL Cancer Institute: EIF4G1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF4G1 in cancer cell metabolism1. de la Parra C, Borrero-Garcia LD, Cruz-Collazo A, Schneider RJ, Dharmawardhane S (2015) Equol, an isoflavone metabolite, regulates cancer cell viability and protein synthesis initiation via c-Myc and eIF4G. J Biol Chem 290: 6047-6057. doi: 10.1074/jbc.M114.617415. pmid: 4358247. go to article
2. Thoreen CC, Chantranupong L, Keys HR, Wang T, Gray NS, et al. (2012) A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485: 109-113. doi: 10.1038/nature11083. pmid: 3347774. go to article
3. Liang S, Zhou Y, Chen Y, Ke G, Wen H, et al. (2014) Decreased expression of EIF4A1 after preoperative brachytherapy predicts better tumor-specific survival in cervical cancer. Int J Gynecol Cancer 24: 908-915. doi: 10.1097/IGC.0000000000000152. go to article
4. Badura M, Braunstein S, Zavadil J, Schneider RJ (2012) DNA damage and eIF4G1 in breast cancer cells reprogram translation for survival and DNA repair mRNAs. Proc Natl Acad Sci U S A 109: 18767-18772. doi: 10.1073/pnas.1203853109. pmid: 3503184. go to article

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Phenotypic Information for EIF4G1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4G1
Familial Cancer Database: EIF4G1
* 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 600495; gene.
600495; gene.
614251; phenotype.
614251; phenotype.
Orphanet 2828; Young adult-onset Parkinsonism.
2828; Young adult-onset Parkinsonism.
DiseaseKEGG Disease: EIF4G1
MedGen: EIF4G1 (Human Medical Genetics with Condition)
ClinVar: EIF4G1
PhenotypeMGI: EIF4G1 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF4G1

Mutations for EIF4G1
* 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 EIF4G1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF734084EIF4G1491663184045002184045120EIF4G11642173184039685184039738
AW859459EIF4G165063184039544184040401TPM250167393568551035685776
AI205494RABEP131891752817955281981EIF4G11885373184039589184040202
AI700104RABEP1152001752817955281981EIF4G11994013184039745184040202
AW859452EIF4G115033184039544184040401TPM249866393568551435685776
AW859462EIF4G174553184039604184040401TPM245050193568572535685776
BF696853RNU6-111073180949525180949632EIF4G11066253184038425184039443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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=14

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=137)
Stat. for Synonymous SNVs
(# total SNVs=34)
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
chr3:184040741-184040741p.K643R13
chr3:184045208-184045208p.T1211T3
chr3:184041675-184041675p.L794L3
chr3:184038427-184038427p.R183*3
chr3:184041274-184041274p.E723K3
chr3:184042723-184042723p.R893W3
chr3:184041028-184041028p.P696L2
chr3:184041364-184041364p.D753N2
chr3:184052638-184052638p.S1581F2
chr3:184040889-184040889p.R650W2

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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
# sample522162 7151 17145 11324113
# mutation523172 9151 22175 11530118
nonsynonymous SNV323131 7 41 12132 11120114
synonymous SNV2  41 211  1043  410 4
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
chr3:184042723p.R698W,EIF4G13
chr3:184045480p.T27M,EIF4G12
chr3:184039537p.S1386F,EIF4G12
chr3:184052538p.E193K,EIF4G12
chr3:184038752p.L1061L,EIF4G12
chr3:184039307p.R13C,EIF4G12
chr3:184052638p.R116H,EIF4G12
chr3:184039405p.L149F,EIF4G12
chr3:184037581p.A1353T,EIF4G12
chr3:184037588p.E691K,EIF4G11

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 EIF4G1 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 EIF4G1

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

ABCF3,AP2M1,DCUN1D1,DVL3,EIF4G1,FBXO45,FXR1,
INCENP,KIAA0226,LSG1,MCCC1,OPA1,PCYT1A,POLR1A,
PSMD2,RFC4,RNF168,SENP5,TBCCD1,TFRC,YEATS2
ABCF1,CUEDC1,DNAJA3,DNAJC11,DPP9,EHBP1L1,EIF4G1,
ESRRA,EVI5L,FLII,FXR2,GBF1,GCN1L1,GTF3C1,
CLUH,MYO18A,PANK4,PLEC,PSMD3,RPTOR,USP5

ARID1A,ATP2A2,PRRC2A,NOP9,CHD4,EIF4G1,EP400,
GCN1L1,HCFC1,INCENP,KMT2B___KMT2D,NSD1,PIK3R4,POLR3A,
PSMD2,RAD54L2,RNF168,SPEN,VPRBP,YEATS2,YLPM1
AP3D1,ATP2A2,BMS1,NOP9,DPP9,EIF4G1,ELAVL1,
GCN1L1,HNRNPM,KHSRP,KPNB1,LARP1,NUP98,PRKDC,
SAFB,SEC16A,SF3B3,TAF15,UGGT1,VARS,XPO5
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 EIF4G1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q04637; -.
ChemistryBindingDB Q04637; -.
Organism-specific databasesPharmGKB PA27722; -.
Organism-specific databasesPharmGKB PA27722; -.
Organism-specific databasesCTD 1981; -.
Organism-specific databasesCTD 1981; -.

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 4 gamma, 1approved; investigationalSirolimus


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Cross referenced IDs for EIF4G1
* 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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