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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 EIF4A1

Basic gene info.	Gene symbol	EIF4A1
	Gene name	eukaryotic translation initiation factor 4A1
	Synonyms	DDX2A\|EIF-4A\|EIF4A\|eIF-4A-I\|eIF4A-I
	Cytomap	UCSC genome browser: 17p13
	Genomic location	chr17 :7476023-7482324
	Type of gene	protein-coding
	RefGenes	NM_001204510.1, NM_001416.3,
	Ensembl id	ENSG00000161960
	Description	ATP-dependent RNA helicase eIF4A-1eukaryotic initiation factor 4A-Ieukaryotic initiation factor 4AIeukaryotic translation initiation factor 4A
	Modification date	20141207
dbXrefs	MIM : 602641
	HGNC : HGNC
	Ensembl : ENSG00000161960
	HPRD : 04030
	Vega : OTTHUMG00000108149
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF4A1
	BioGPS: 1973
	Gene Expression Atlas: ENSG00000161960
	The Human Protein Atlas: ENSG00000161960
Pathway	NCI Pathway Interaction Database: EIF4A1
	KEGG: EIF4A1
	REACTOME: EIF4A1
	ConsensusPathDB
	Pathway Commons: EIF4A1
Metabolism	MetaCyc: EIF4A1
	HUMANCyc: EIF4A1
Regulation	Ensembl's Regulation: ENSG00000161960
	miRBase: chr17 :7,476,023-7,482,324
	TargetScan: NM_001204510
	cisRED: ENSG00000161960
Context	iHOP: EIF4A1
	cancer metabolism search in PubMed: EIF4A1
	UCL Cancer Institute: EIF4A1
Assigned class in ccmGDB	C

Top

Phenotypic Information for EIF4A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF4A1
	Familial Cancer Database: EIF4A1

* 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
Orphanet
Disease	KEGG Disease: EIF4A1
	MedGen: EIF4A1 (Human Medical Genetics with Condition)
	ClinVar: EIF4A1
Phenotype	MGI: EIF4A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF4A1

Mutations for EIF4A1

* 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 EIF4A1 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
CN430498	FAM120A	1	242	9	96278379	96289505	EIF4A1	238	300	17	7482162	7482224
BC006380	NRF1	21	409	7	129351313	129367207	EIF4A1	407	1574	17	7478436	7482036
BQ670981	CTSL1	1	556	9	90343574	90346046	EIF4A1	551	840	17	7481876	7482163
CB119692	TRAF7	40	248	16	2227838	2228046	EIF4A1	246	416	17	7482008	7482179
AI371755	EIF4A1	1	330	17	7481702	7482031	HSPA2	325	384	14	65009163	65009222
CD049225	RPL37A	10	88	2	217366106	217366184	EIF4A1	89	889	17	7477605	7480964
AU119214	EIF4A1	1	291	17	7480337	7480805	EIF4A1	292	788	17	7476144	7478035

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=4

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted snv.

Top

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
chr17:7476179-7476179	p.S7F	4
chr17:7477965-7477965	p.I58I	2
chr17:7480012-7480012	p.?	2
chr17:7480906-7480906	p.L263R	2
chr17:7480414-7480414	p.D185D	2
chr17:7476181-7476181	p.R8*	2
chr17:7480777-7480777	p.R247H	1
chr17:7477962-7477963	p.A57_I58insVFRDV	1
chr17:7480995-7480995	p.H293D	1
chr17:7479928-7479928	p.V144V	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

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		3		1		1					2	4	3			1	3	1	6
# mutation	1		3		1		1					2	5	3			1	3	1	6
nonsynonymous SNV	1		1		1		1					2	5	1			1	1		4
synonymous SNV			2											2				2	1	2

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])

Top

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
chr17:7478537	p.V144V,EIF4A1	1
chr17:7480995	p.W343C,EIF4A1	1
chr17:7479876	p.D185D,EIF4A1	1
chr17:7481145	p.I387I	1
chr17:7479928	p.T207T,EIF4A1	1
chr17:7481183	p.E388Q	1
chr17:7480414	p.P217H,EIF4A1	1
chr17:7481234	p.R247H,EIF4A1	1
chr17:7476160	p.R255L,EIF4A1	1
chr17:7480480	p.T269N,EIF4A1	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 EIF4A1 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]

Top

Gene Expression for EIF4A1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


AURKB,C1QBP,CTDNEP1,EIF4A1,EIF5A,EIF5AL1,ELAC2, FXR2,MYBBP1A,NUP88,OVCA2,PELP1,PFN1,PSMB6, RNMTL1,RPL26,SCO1,SENP3,SLC25A11,TIMM22,WRAP53	APEX1,BYSL,CCT3,DDOST,EIF4A1,ERGIC3,ILF2, METTL1,MRTO4,NHP2,NME1,NOP16,NPM3,PES1, POLR1C,PPIA,PRELID1,RAN,RPL7A,RUVBL1,SNRPD1

ATPAF2,ELP5,C1QBP,COPS3,EIF4A1,EIF5A,EIF5AL1, ELAC2,GEMIN4,MED11,MPDU1,PFN1,PRPSAP2,PSMB6, RNMTL1,SCO1,SLC25A11,TIMM22,TSR1,WRAP53,YWHAE	HYPK,C19orf10,CCT2,EMC8,EBNA1BP2,EIF3I,EIF4A1, EIF5AL1,H2AFZ,HNRNPF,NME1,NPM3,PDIA6,PPIB, PSMD14,PYCRL,RAN,RANBP1,RPL26L1,SNRPD1,SRPRB

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for EIF4A1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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 4A1	approved; investigational	Sirolimus
DB01033	eukaryotic translation initiation factor 4A1	approved	Mercaptopurine
DB00563	eukaryotic translation initiation factor 4A1	approved	Methotrexate

Top

Cross referenced IDs for EIF4A1

* 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