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 EIF5B

Basic gene info.	Gene symbol	EIF5B
	Gene name	eukaryotic translation initiation factor 5B
	Synonyms	IF2
	Cytomap	UCSC genome browser: 2q11.2
	Genomic location	chr2 :99953833-100016728
	Type of gene	protein-coding
	RefGenes	NM_015904.3,
	Ensembl id	ENSG00000158417
	Description	eIF-5Btranslation initiation factor IF-2translation initiation factor IF2
	Modification date	20141207
dbXrefs	MIM : 606086
	HGNC : HGNC
	Ensembl : ENSG00000158417
	HPRD : 07304
	Vega : OTTHUMG00000153242
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF5B
	BioGPS: 9669
	Gene Expression Atlas: ENSG00000158417
	The Human Protein Atlas: ENSG00000158417
Pathway	NCI Pathway Interaction Database: EIF5B
	KEGG: EIF5B
	REACTOME: EIF5B
	ConsensusPathDB
	Pathway Commons: EIF5B
Metabolism	MetaCyc: EIF5B
	HUMANCyc: EIF5B
Regulation	Ensembl's Regulation: ENSG00000158417
	miRBase: chr2 :99,953,833-100,016,728
	TargetScan: NM_015904
	cisRED: ENSG00000158417
Context	iHOP: EIF5B
	cancer metabolism search in PubMed: EIF5B
	UCL Cancer Institute: EIF5B
Assigned class in ccmGDB	C

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Phenotypic Information for EIF5B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF5B
	Familial Cancer Database: EIF5B

* 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
Orphanet
Disease	KEGG Disease: EIF5B
	MedGen: EIF5B (Human Medical Genetics with Condition)
	ClinVar: EIF5B
Phenotype	MGI: EIF5B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF5B

Mutations for EIF5B

* 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

There's no inter-chromosomal structural variation.

- 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	EIF5B	chr2	100010407	100010427	REV1	chr2	100087420	100087440
ovary	EIF5B	chr2	99973957	99973977		chr2	99926623	99926643
pancreas	EIF5B	chr2	99968218	99968238	EIF5B	chr2	99968711	99968731

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 EIF5B 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
AI065143	ATP6V0E1	63	525	5	172461433	172461895	EIF5B	514	537	2	100003799	100003846
BM727161	OLFML2A	1	247	9	127574101	127574347	EIF5B	243	465	2	99984997	99988193
AW839731	EIF5B	56	222	2	99980154	99980326	EIF5B	208	285	2	99988116	99988193
CB243572	EIF5B	14	357	2	99984951	99992883	CCDC113	356	665	16	58317310	58317619
AI739405	EIF5B	105	282	2	99992922	99993099	GCN1L1	276	400	12	120565542	120565666
BE671617	EIF5B	27	317	2	99980857	99988192	TXNDC9	303	543	2	99954023	99977012
AA687907	EIF5B	1	361	2	100006182	100016237	EIF5B	355	438	2	99999332	100006211
DA619466	AFF3	2	384	2	100720864	100759048	EIF5B	384	595	2	99976698	99977012
AI699584	EIF5B	1	53	2	99976741	99976793	EIF5B	48	189	2	99976932	99977671
AW081923	EIF5B	1	246	2	99980114	99980770	EIF5B	227	569	2	99980202	99985023

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=75)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=8)	Stat. for Insertions (# total SNVs=1)

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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
chr2:99976805-99976805	p.K50fs*10	5
chr2:100010862-100010862	p.?	3
chr2:99977965-99977965	p.N203fs*10	3
chr2:100011204-100011204	p.D1038N	3
chr2:99976980-99976980	p.I72V	3
chr2:100007118-100007118	p.Q900K	3
chr2:100015222-100015222	p.I1135I	2
chr2:100007120-100007120	p.Q900H	2
chr2:99999328-99999328	p.E739K	2
chr2:100007161-100007161	p.R914Q	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=5

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	4	1	14			3		1	3		10	1	1		1	2	9		10
# mutation	8	4	1	13			3		1	3		15	1	1		1	2	10		14
nonsynonymous SNV	6	3	1	9			3			1		12	1	1		1	1	6		13
synonymous SNV	2	1		5					1	2		3					1	4		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
chr2:100007118	p.Q900K	2
chr2:100011204	p.V281V	2
chr2:99978207	p.Q900H	2
chr2:100007120	p.R815S	2
chr2:100006721	p.D1038N	2
chr2:100013282	p.V1039V	1
chr2:99988138	p.S135Y	1
chr2:99977707	p.K442K	1
chr2:99998633	p.D721H	1
chr2:100006829	p.L877F	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 EIF5B 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 EIF5B

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


CCDC58,DNAJC2,EIF5B,FAM136A,GEMIN6,GNL2,MAGOH, MEMO1,MPHOSPH10,MRPS9,NDUFS5,NOL10,NOP58,NUTF2, PDCL3,PDSS1,RPP40,SNRPG,SSB,SSBP1,UTP11L	C6orf203,CWC27,DNAJC7,DNAJC8,EIF2S2,EIF4E2,EIF5B, FAM118B,HTATSF1,LSM1,PRPS1,PSMC2,PSMD1,PSMD7, RBM17,SBDS,TTC1,UBC,UBE2G2,XPA,ZCRB1

CCAR1,CWC22,EIF5B,HNRNPA2B1,HNRNPA3,HNRNPU,IWS1, LTV1,MPHOSPH10,MRPS5,MRPS9,NCL,NOP58,POU2F1, PPIG,PPM1G,RPF2,SSB,TARDBP,WDR75,WDR92	ADAMTS9,AKAP12,ARMCX3,CELF2,DDX19A,DDX24,DYX1C1, EIF5B,LBR,NAV2,NUCKS1,OXCT1,PBRM1,PRKAR1A, PTPN11,ROCK1,SEC63,SRP68,SUPT16H,TCOF1,ZC3H13

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 EIF5B

There's no related Drug.

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Cross referenced IDs for EIF5B

* 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