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 EIF5A

Basic gene info.	Gene symbol	EIF5A
	Gene name	eukaryotic translation initiation factor 5A
	Synonyms	EIF-5A\|EIF5A1\|eIF5AI
	Cytomap	UCSC genome browser: 17p13-p12
	Genomic location	chr17 :7210855-7215782
	Type of gene	protein-coding
	RefGenes	NM_001143760.1, NM_001143761.1,NM_001143762.1,NM_001970.4,
	Ensembl id	ENSG00000132507
	Description	eIF-4DeIF-5A-1eIF-5A1eukaryotic initiation factor 5Aeukaryotic translation initiation factor 5A-1rev-binding factor
	Modification date	20141207
dbXrefs	MIM : 600187
	HGNC : HGNC
	Ensembl : ENSG00000132507
	HPRD : 02555
	Vega : OTTHUMG00000102197
Protein	UniProt: P63241 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF5A
	BioGPS: 1984
	Gene Expression Atlas: ENSG00000132507
	The Human Protein Atlas: ENSG00000132507
Pathway	NCI Pathway Interaction Database: EIF5A
	KEGG: EIF5A
	REACTOME: EIF5A
	ConsensusPathDB
	Pathway Commons: EIF5A
Metabolism	MetaCyc: EIF5A
	HUMANCyc: EIF5A
Regulation	Ensembl's Regulation: ENSG00000132507
	miRBase: chr17 :7,210,855-7,215,782
	TargetScan: NM_001143760
	cisRED: ENSG00000132507
Context	iHOP: EIF5A
	cancer metabolism search in PubMed: EIF5A
	UCL Cancer Institute: EIF5A
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF5A in cancer cell metabolism	1. Memin E, Hoque M, Jain MR, Heller DS, Li H, et al. (2014) Blocking eIF5A modification in cervical cancer cells alters the expression of cancer-related genes and suppresses cell proliferation. Cancer Res 74: 552-562. doi: 10.1158/0008-5472.CAN-13-0474. go to article 2. Xu G, Yu H, Shi X, Sun L, Zhou Q, et al. (2014) Cisplatin sensitivity is enhanced in non-small cell lung cancer cells by regulating epithelial-mesenchymal transition through inhibition of eukaryotic translation initiation factor 5A2. BMC Pulm Med 14: 174. doi: 10.1186/1471-2466-14-174. pmid: 4232729. go to article 3. Mittal N, Morada M, Tripathi P, Gowri VS, Mandal S, et al. (2014) Cryptosporidium parvum has an active hypusine biosynthesis pathway. Mol Biochem Parasitol 195: 14-22. doi: 10.1016/j.molbiopara.2014.05.005. pmid: 4176827. go to article 4. Dyshlovoy SA, Venz S, Shubina LK, Fedorov SN, Walther R, et al. (2014) Activity of aaptamine and two derivatives, demethyloxyaaptamine and isoaaptamine, in cisplatin-resistant germ cell cancer. J Proteomics 96: 223-239. doi: 10.1016/j.jprot.2013.11.009. go to article

Top

Phenotypic Information for EIF5A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF5A
	Familial Cancer Database: EIF5A

* 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	600187; gene.
Orphanet
Disease	KEGG Disease: EIF5A
	MedGen: EIF5A (Human Medical Genetics with Condition)
	ClinVar: EIF5A
Phenotype	MGI: EIF5A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF5A

Mutations for EIF5A

* 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

Top

- 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
ovary	EIF5A	chr17	7215419	7215439	NBEA	chr13	35987643	35987663

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 EIF5A 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
CN372949	FKBP4	2	51	12	2904302	2904351	EIF5A	49	295	17	7211044	7214369
BF883338	TCOF1	12	170	5	149776379	149778618	EIF5A	166	402	17	7213103	7213339
CN336887	EIF5A	1	239	17	7214910	7215318	SGSM3	233	344	22	40800416	40800628
AW954202	EIF5A	1	56	17	7215346	7215401	HSF1	57	196	8	145538241	145538380
BG255468	EIF5A	1	363	17	7210928	7214368	RALY	361	398	20	32602679	32602717
BM720324	EIF5A	9	208	17	7215434	7215633	ADAR	209	443	1	154555010	154555244
CN340509	EIF5A	5	80	17	7212934	7213009	DNAJC24	81	572	11	31391414	31436658

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

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

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=5

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=18)	Stat. for Synonymous SNVs (# total SNVs=1)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted 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
chr17:7213030-7213030	p.R26C	4
chr17:7212975-7212975	p.F7F	2
chr17:7213034-7213034	p.K27T	2
chr17:7212956-7212956	p.M1R	2
chr17:7214942-7214942	p.K150E	1
chr17:7214392-7214392	p.P74L	1
chr17:7214946-7214946	p.A151V	1
chr17:7212989-7212989	p.A12V	1
chr17:7214674-7214674	p.I92I	1
chr17:7214949-7214949	p.M152T	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

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	5		6
# mutation			1	3					1			1					2	5		7
nonsynonymous SNV			1	3					1			1						4		6
synonymous SNV																	2	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])

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
chr17:7212975	p.F37F,EIF5A	2
chr17:7214700	p.A42V,EIF5A	1
chr17:7212989	p.M182T,EIF5A	1
chr17:7214735	p.A46A,EIF5A	1
chr17:7213002	p.R56C,EIF5A	1
chr17:7214927	p.S76L,EIF5A	1
chr17:7213030	p.G79C,EIF5A	1
chr17:7214941	p.G82S,EIF5A	1
chr17:7213091	p.G82D,EIF5A	1
chr17:7214942	p.P104L,EIF5A	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 EIF5A 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 EIF5A

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


CALD1,CLIC4,CSGALNACT2,DACT1,DPYSL3,DSE,EIF5A2, FAP,FERMT2,FNDC3B,FSTL1,IKBIP,ITGB1,LATS2, LOX,PKD2,PLS3,RECK,SEC23A,TIMP2,TRPC1	BNIP2,CCDC82,CLIC2,CLIC4,CPNE8,EIF5A2,EVI5, KCTD12,LRCH2,LRRC8C,MYCT1,BBIP1,PTPN12,RAB8B, RAP1B,RBMS1,SEPT7,SGMS1,SGTB,SHE,TMX3

ADO,ADIRF,C19orf38,CA6,CCK,DNM1,EIF5A2, HGFAC,INSIG2,KIAA0895,MAP1LC3B2,NDFIP1,NRBF2,PAK7, PRRG1,SAR1A,SOHLH1,TCHH,TEX19,ZNF735,ZNF83	BLVRA,FAM229B,EIF5A2,FAM195B,FEZ1,GNB4,GUCY1B3, HDGFRP3,LOC399959,LOC644538,MRAS,SLC9B2,NME4,RAB23, RAB31,IFT22,RHOQ,RND2,SNCA,SPG20,ZNF25

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 EIF5A

There's no related Drug.

Top

Cross referenced IDs for EIF5A

* 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