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 EIF4A2

Basic gene info.	Gene symbol	EIF4A2
	Gene name	eukaryotic translation initiation factor 4A2
	Synonyms	BM-010\|DDX2B\|EIF4A\|EIF4F\|eIF-4A-II\|eIF4A-II
	Cytomap	UCSC genome browser: 3q28
	Genomic location	chr3 :186501360-186507685
	Type of gene	protein-coding
	RefGenes	NM_001967.3,
	Ensembl id	ENSG00000156976
	Description	ATP-dependent RNA helicase eIF4A-2eukaryotic initiation factor 4A-II
	Modification date	20141207
dbXrefs	MIM : 601102
	HGNC : HGNC
	Ensembl : ENSG00000156976
	HPRD : 03062
	Vega : OTTHUMG00000156564
Protein	UniProt: Q14240 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF4A2
	BioGPS: 1974
	Gene Expression Atlas: ENSG00000156976
	The Human Protein Atlas: ENSG00000156976
Pathway	NCI Pathway Interaction Database: EIF4A2
	KEGG: EIF4A2
	REACTOME: EIF4A2
	ConsensusPathDB
	Pathway Commons: EIF4A2
Metabolism	MetaCyc: EIF4A2
	HUMANCyc: EIF4A2
Regulation	Ensembl's Regulation: ENSG00000156976
	miRBase: chr3 :186,501,360-186,507,685
	TargetScan: NM_001967
	cisRED: ENSG00000156976
Context	iHOP: EIF4A2
	cancer metabolism search in PubMed: EIF4A2
	UCL Cancer Institute: EIF4A2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF4A2 in cancer cell metabolism	1. Yan LX, Wu QN, Zhang Y, Li YY, Liao DZ, et al. (2011) Knockdown of miR-21 in human breast cancer cell lines inhibits proliferation, in vitro migration and in vivo tumor growth. Breast Cancer Res 13: R2. doi: 10.1186/bcr2803. pmid: 3109565. go to article 2. Shaoyan X, Juanjuan Y, Yalan T, Ping H, Jianzhong L, et al. (2013) Downregulation of EIF4A2 in non-small-cell lung cancer associates with poor prognosis. Clin Lung Cancer 14: 658-665. doi: 10.1016/j.cllc.2013.04.011. go to article

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Phenotypic Information for EIF4A2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF4A2
	Familial Cancer Database: EIF4A2

* 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	601102; gene.
Orphanet
Disease	KEGG Disease: EIF4A2
	MedGen: EIF4A2 (Human Medical Genetics with Condition)
	ClinVar: EIF4A2
Phenotype	MGI: EIF4A2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF4A2

Mutations for EIF4A2

* 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

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

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 EIF4A2 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
BF990739	DLG5	14	119	10	79579707	79584177	EIF4A2	119	295	3	186502123	186502299
DA558800	EIF4A2	1	68	3	186505472	186505539	LMNA	69	549	1	156084526	156085006
BM773122	EIF4A2	20	415	3	186504914	186506183	FUS	410	506	16	31202784	31202880
BM781579	EIF4A2	20	414	3	186504914	186506183	FUS	409	551	16	31202784	31202926
AW840050	EIF4A2	6	297	3	186505669	186505963	EIF4A2	292	342	3	186505654	186505704
BG979271	EIF4A2	9	311	3	186506486	186506792	EIF4A2	305	377	3	186506836	186506908
BQ355782	KIAA1217	13	186	10	24833139	24833314	EIF4A2	176	450	3	186507348	186507622
AI810008	ATP6V1C2	7	148	2	10923517	10923658	EIF4A2	141	543	3	186506429	186506831
DA027118	EIF4A2	1	463	3	186501366	186503752	TGFBI	464	557	5	135364680	135364773
BM834299	EIF4A2	1	69	3	186501368	186501436	PPDPF	65	562	20	62153365	62153862
BF840289	ACTR2	77	313	2	65497286	65497523	EIF4A2	312	501	3	186506064	186506253
BF987336	DLG5	14	119	10	79579707	79584177	EIF4A2	119	295	3	186502123	186502299

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=50)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr3:186503976-186503976	p.V181L	3
chr3:186504345-186504345	p.F228I	2
chr3:186503977-186503977	p.V181A	2
chr3:186504030-186504030	p.E199K	2
chr3:186506990-186506990	p.R386G	2
chr3:186503790-186503790	p.V156D	1
chr3:186505363-186505368	p.T330_L332>M	1
chr3:186501404-186501404	p.S2C	1
chr3:186504342-186504342	p.K227Q	1
chr3:186506999-186506999	p.E389K	1

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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=4

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	1	4		12			1		3			5	3	2			5	4		6
# mutation	1	4		8			1		3			5	3	2			5	4		7
nonsynonymous SNV	1	4		7					3			4	2	2			2	4		6
synonymous SNV				1			1					1	1				3			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
chr3:186506990	p.R386S	3
chr3:186505659	p.N356T	2
chr3:186503977	p.V181A	2
chr3:186504993	p.T352S	1
chr3:186502263	p.D33N	1
chr3:186505599	p.T272T	1
chr3:186503978	p.P66P	1
chr3:186504995	p.F279S	1
chr3:186502264	p.I358V	1
chr3:186505633	p.I89V	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 EIF4A2 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 EIF4A2

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


BCL2,EFCAB7,EIF2A,EIF4A2,FXR1,MBLAC2,MED13L, MYEF2,PHF21A,RABGGTB,SCAPER,SENP2,SLC25A36,THAP2, TYW3,VPS8,ZSCAN26,ZNF24,ZNF33B,ZRANB2,ZSWIM6	ABCB7,ATAD1,FOPNL,TRMT1L,CCNG1,CNOT4,COPS2, CRBN,DCTN4,DYM,EIF4A2,EIF4B,FAM175A,GIN1, POLR2M___GCOM1,LIAS,LRPPRC,PHF10,RCOR3,TRIM23,ZRANB1

ZFAS1,C3orf17,EEF1B2,EIF2A,EIF4A2,MYNN,NMD3, RPL10A,RPL12,RPL15,RPL24,RPL32,RPL35A,RPL7A, RPS11,RPS15A,RPS18,RPS3A,RYK,SERP1,SLC25A36	AMZ2P1,ARL3,BBS10,BEX4,CAMLG,COMMD6,EIF4A2, FAM175A,IFT46,LZTFL1,MEAF6,PCMTD1,RRAGB,RYK, SNRPN,SPATA7,TCEAL1,TCEAL8,UBE2Q2,ZSCAN26,ZNF691

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 EIF4A2

There's no related Drug.

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Cross referenced IDs for EIF4A2

* 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