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 EEF1B2

Basic gene info.	Gene symbol	EEF1B2
	Gene name	eukaryotic translation elongation factor 1 beta 2
	Synonyms	EEF1B\|EEF1B1\|EF1B
	Cytomap	UCSC genome browser: 2q33.3
	Genomic location	chr2 :207024317-207027653
	Type of gene	protein-coding
	RefGenes	NM_001037663.1, NM_001959.3,NM_021121.3,
	Ensembl id	ENSG00000114942
	Description	EF-1-betaelongation factor 1-betaeukaryotic translation elongation factor 1 beta 1
	Modification date	20141207
dbXrefs	MIM : 600655
	HGNC : HGNC
	Ensembl : ENSG00000114942
	HPRD : 02804
	Vega : OTTHUMG00000132891
Protein	UniProt: P24534 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EEF1B2
	BioGPS: 1933
	Gene Expression Atlas: ENSG00000114942
	The Human Protein Atlas: ENSG00000114942
Pathway	NCI Pathway Interaction Database: EEF1B2
	KEGG: EEF1B2
	REACTOME: EEF1B2
	ConsensusPathDB
	Pathway Commons: EEF1B2
Metabolism	MetaCyc: EEF1B2
	HUMANCyc: EEF1B2
Regulation	Ensembl's Regulation: ENSG00000114942
	miRBase: chr2 :207,024,317-207,027,653
	TargetScan: NM_001037663
	cisRED: ENSG00000114942
Context	iHOP: EEF1B2
	cancer metabolism search in PubMed: EEF1B2
	UCL Cancer Institute: EEF1B2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for EEF1B2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EEF1B2
	Familial Cancer Database: EEF1B2

* 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	600655; gene.
Orphanet
Disease	KEGG Disease: EEF1B2
	MedGen: EEF1B2 (Human Medical Genetics with Condition)
	ClinVar: EEF1B2
Phenotype	MGI: EEF1B2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EEF1B2

Mutations for EEF1B2

* 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 EEF1B2 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
BE783880	BLCAP	32	399	20	36151714	36152082	EEF1B2	382	747	2	207026773	207027624
DA486448	EEF1B2	5	511	2	207024621	207027239	CDR1	504	562	X	139866568	139866626

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=30

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=38)	Stat. for Synonymous SNVs (# total SNVs=25)

Stat. for Deletions (# total SNVs=2)	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
chr2:207025358-207025358	p.S43G	30
chr2:207025366-207025366	p.P45P	28
chr2:207027489-207027490	p.L187fs*7	2
chr2:207025444-207025444	p.?	2
chr2:207027283-207027283	p.A156A	2
chr2:207027455-207027455	p.K176E	2
chr2:207025408-207025408	p.I59M	1
chr2:207026798-207026798	p.L123V	1
chr2:207027530-207027530	p.D201H	1
chr2:207027212-207027212	p.?	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=28

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	1		2					2	2		9	1		2	5	5	6	2	6
# mutation	2	1		2					2	1		4	1		2	2	2	4	2	6
nonsynonymous SNV	2	1		2					1	1		3			1	1	1	3	1	4
synonymous SNV									1			1	1		1	1	1	1	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])

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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
chr2:207025358	p.S43G,EEF1B2	28
chr2:207025366	p.P45P,EEF1B2	22
chr2:207027283	p.A156A,EEF1B2	2
chr2:207026135	p.P46S,EEF1B2	1
chr2:207026140	p.K74T,EEF1B2	1
chr2:207026150	p.S90T,EEF1B2	1
chr2:207026796	p.A92T,EEF1B2	1
chr2:207027266	p.S95T,EEF1B2	1
chr2:207024769	p.R122H,EEF1B2	1
chr2:207027298	p.D151N,EEF1B2	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 EEF1B2 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 EEF1B2

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


EEF1B2,EEF1G,RPL10A,RPL11,RPL12,RPL17,RPL31, RPL3,RPL37A,RPL4,RPL5,RPL6,RPL7A,RPS10, RPS13,RPS18,RPS25,RPS27A,RPS8,RPSA,RPSAP58	EEF1B2,EEF1G,GNB2L1,NACA,RPL10,RPL10A,RPL12, RPL14,RPL37,RPL4,RPL5,RPL6,RPLP0,RPS14, RPS18,RPS2,RPS3A,RPS6,RPS7,RPS8,RPSAP58

EEF1B2,RPL10A,RPL15,RPL32,RPL35,RPL35A,RPL36, RPS10,RPS11,RPS13,RPS14,RPS15A,RPS18,RPS3, RPS3A,RPS5,RPS6,RPS7,RPSA,RPSAP58,RSL24D1	C1orf43,ATRAID,DPY30,EEF1B2,GPN1,RPL24,RPL27A, RPS10,RPS13,RPS14,RPS18,RPS21,RPS3,RPS3A, RPS5,RPS6,RPS7,RPS8,TMEM14B,TMEM14C,TPT1

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 EEF1B2

There's no related Drug.

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Cross referenced IDs for EEF1B2

* 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