Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 EIF4G1

Basic gene info.	Gene symbol	EIF4G1
	Gene name	eukaryotic translation initiation factor 4 gamma, 1
	Synonyms	EIF-4G1\|EIF4F\|EIF4G\|EIF4GI\|P220\|PARK18
	Cytomap	UCSC genome browser: 3q27.1
	Genomic location	chr3 :184032282-184053146
	Type of gene	protein-coding
	RefGenes	NM_001194946.1, NM_001194947.1,NM_001291157.1,NM_004953.4,NM_182917.4, NM_198241.2,NM_198242.2,NM_198244.2,
	Ensembl id	ENSG00000114867
	Description	EIF4-gammaeIF-4-gamma 1eucaryotic translation initiation factor 4Geukaryotic translation initiation factor 4 gamma 1
	Modification date	20141207
dbXrefs	MIM : 600495
	HGNC : HGNC
	Ensembl : ENSG00000114867
	HPRD : 06774
	Vega : OTTHUMG00000156784
Protein	UniProt: Q04637 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF4G1
	BioGPS: 1981
	Gene Expression Atlas: ENSG00000114867
	The Human Protein Atlas: ENSG00000114867
Pathway	NCI Pathway Interaction Database: EIF4G1
	KEGG: EIF4G1
	REACTOME: EIF4G1
	ConsensusPathDB
	Pathway Commons: EIF4G1
Metabolism	MetaCyc: EIF4G1
	HUMANCyc: EIF4G1
Regulation	Ensembl's Regulation: ENSG00000114867
	miRBase: chr3 :184,032,282-184,053,146
	TargetScan: NM_001194946
	cisRED: ENSG00000114867
Context	iHOP: EIF4G1
	cancer metabolism search in PubMed: EIF4G1
	UCL Cancer Institute: EIF4G1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF4G1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	600495; gene. 600495; gene. 614251; phenotype. 614251; phenotype.
Orphanet	2828; Young adult-onset Parkinsonism. 2828; Young adult-onset Parkinsonism.
Disease	KEGG Disease: EIF4G1
	MedGen: EIF4G1 (Human Medical Genetics with Condition)
	ClinVar: EIF4G1
Phenotype	MGI: EIF4G1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF4G1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BF734084	EIF4G1	49	166	3	184045002	184045120	EIF4G1	164	217	3	184039685	184039738
AW859459	EIF4G1	6	506	3	184039544	184040401	TPM2	501	673	9	35685510	35685776
AI205494	RABEP1	3	189	17	5281795	5281981	EIF4G1	188	537	3	184039589	184040202
AI700104	RABEP1	15	200	17	5281795	5281981	EIF4G1	199	401	3	184039745	184040202
AW859452	EIF4G1	1	503	3	184039544	184040401	TPM2	498	663	9	35685514	35685776
AW859462	EIF4G1	7	455	3	184039604	184040401	TPM2	450	501	9	35685725	35685776
BF696853	RNU6-1	1	107	3	180949525	180949632	EIF4G1	106	625	3	184038425	184039443
AI744700	PPP1R14A	1	165	19	38741882	38742046	EIF4G1	161	430	3	184046457	184049153
AU133771	EIF4G1	10	361	3	184040396	184040965	EIF4G1	359	762	3	184038480	184039375
BQ212371	EIF4G1	1	104	3	184042831	184043088	EIF4G1	98	720	3	184042116	184043724
BQ016901	UCP2	19	265	11	73685717	73685963	EIF4G1	257	399	3	184045158	184045437
DA536097	MYO18A	1	473	17	27435487	27435960	EIF4G1	464	520	3	184043146	184043307
AI656047	RABEP1	3	189	17	5281795	5281981	EIF4G1	188	635	3	184039494	184040202
BQ009628	EIF4G1	17	213	3	184052945	184053141	MCC	212	728	5	112379256	112389659
BE501999	RABEP1	3	189	17	5281795	5281981	EIF4G1	188	676	3	184039456	184040202
DA453269	EIF4G1	1	140	3	184035272	184037517	EIF4G1	129	567	3	184033920	184043666
F00479	MIR548N	2	71	2	179484435	179484504	EIF4G1	68	268	3	184046459	184049086
BE466786	RABEP1	3	189	17	5281795	5281981	EIF4G1	188	633	3	184039498	184040202
BE077006	EIF4G1	14	402	3	184052077	184052470	HELLS	394	632	10	96326010	96326248
BE466214	RABEP1	3	189	17	5281795	5281981	EIF4G1	188	670	3	184039462	184040202
AK098133	RAP1A	1	519	1	112193133	112193650	EIF4G1	518	2322	3	184045905	184052842

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr3:184040741-184040741	p.K643R	13
chr3:184045208-184045208	p.T1211T	3
chr3:184041675-184041675	p.L794L	3
chr3:184038427-184038427	p.R183*	3
chr3:184041274-184041274	p.E723K	3
chr3:184042723-184042723	p.R893W	3
chr3:184041028-184041028	p.P696L	2
chr3:184041364-184041364	p.D753N	2
chr3:184052638-184052638	p.S1581F	2
chr3:184040889-184040889	p.R650W	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	5	2	2	16	2		7	1	5	1		17	14	5		1	13	24	1	13
# mutation	5	2	3	17	2		9	1	5	1		22	17	5		1	15	30	1	18
nonsynonymous SNV	3	2	3	13	1		7		4	1		12	13	2		1	11	20	1	14
synonymous SNV	2			4	1		2	1	1			10	4	3			4	10		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:184042723	p.R698W,EIF4G1	3
chr3:184045480	p.T27M,EIF4G1	2
chr3:184039537	p.S1386F,EIF4G1	2
chr3:184052538	p.E193K,EIF4G1	2
chr3:184038752	p.L1061L,EIF4G1	2
chr3:184039307	p.R13C,EIF4G1	2
chr3:184052638	p.R116H,EIF4G1	2
chr3:184039405	p.L149F,EIF4G1	2
chr3:184037581	p.A1353T,EIF4G1	2
chr3:184044407	p.S1371G,EIF4G1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q04637; -.
Chemistry	BindingDB	Q04637; -.
Organism-specific databases	PharmGKB	PA27722; -.
Organism-specific databases	PharmGKB	PA27722; -.
Organism-specific databases	CTD	1981; -.
Organism-specific databases	CTD	1981; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00877	eukaryotic translation initiation factor 4 gamma, 1	approved; investigational	Sirolimus

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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