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 EIF3E

Basic gene info.	Gene symbol	EIF3E
	Gene name	eukaryotic translation initiation factor 3, subunit E
	Synonyms	EIF3-P48\|EIF3S6\|INT6\|eIF3-p46
	Cytomap	UCSC genome browser: 8q22-q23
	Genomic location	chr8 :109213971-109260959
	Type of gene	protein-coding
	RefGenes	NM_001568.2,
	Ensembl id	ENSG00000104408
	Description	eIF-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 date	20141222
dbXrefs	MIM : 602210
	HGNC : HGNC
	Ensembl : ENSG00000104408
	HPRD : 03734
	Vega : OTTHUMG00000164858
Protein	UniProt: P60228 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3E
	BioGPS: 3646
	Gene Expression Atlas: ENSG00000104408
	The Human Protein Atlas: ENSG00000104408
Pathway	NCI Pathway Interaction Database: EIF3E
	KEGG: EIF3E
	REACTOME: EIF3E
	ConsensusPathDB
	Pathway Commons: EIF3E
Metabolism	MetaCyc: EIF3E
	HUMANCyc: EIF3E
Regulation	Ensembl's Regulation: ENSG00000104408
	miRBase: chr8 :109,213,971-109,260,959
	TargetScan: NM_001568
	cisRED: ENSG00000104408
Context	iHOP: EIF3E
	cancer metabolism search in PubMed: EIF3E
	UCL Cancer Institute: EIF3E
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF3E in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	602210; gene.
Orphanet
Disease	KEGG Disease: EIF3E
	MedGen: EIF3E (Human Medical Genetics with Condition)
	ClinVar: EIF3E
Phenotype	MGI: EIF3E (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	EIF3E	chr8	109241051	109241071	EIF3E	chr8	109241866	109241886
ovary	EIF3E	chr8	109260140	109260160		chr8	109296582	109296602

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF3E 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
DA000478	EIF3E	1	129	8	109254115	109260942	GTSE1	128	525	22	46693275	46704453
BF799939	EIF3E	17	272	8	109228642	109240524	PRSS23	264	662	11	86519299	86519699

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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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=11

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Somatic 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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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
chr8:109240603-109240603	p.L205L	6
chr8:109240604-109240604	p.L205P	5
chr8:109215229-109215229	p.Q428*	3
chr8:109248412-109248412	p.D115G	2
chr8:109241355-109241355	p.N181D	2
chr8:109260856-109260856	p.L26I	2
chr8:109226865-109226865	p.F344F	2
chr8:109252288-109252288	p.R74S	2
chr8:109260902-109260902	p.I10I	2
chr8:109241421-109241421	p.P159T	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=11

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	2	3	3	17	1		2		1	1		6	6	4			2	2		7
# mutation	2	3	3	8	1		2		1	1		6	7	4			2	2		11
nonsynonymous SNV		1	2	6	1		2		1			4	6	4			1	1		10
synonymous SNV	2	2	1	2						1		2	1				1	1		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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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
chr8:109240603	p.L205L	6
chr8:109240604	p.L205P	5
chr8:109215282	p.I10I	2
chr8:109260902	p.S410N	2
chr8:109241378	p.K407N	1
chr8:109226942	p.L235L	1
chr8:109254087	p.G171R	1
chr8:109240547	p.K407T	1
chr8:109215290	p.D234Y	1
chr8:109241385	p.A165T	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 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

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


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

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 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