Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 EEF2
Basic gene info.Gene symbolEEF2
Gene nameeukaryotic translation elongation factor 2
SynonymsEEF-2|EF-2|EF2|SCA26
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :3976053-3985461
Type of geneprotein-coding
RefGenesNM_001961.3,
Ensembl idENSG00000167658
Descriptionelongation factor 2polypeptidyl-tRNA translocase
Modification date20141207
dbXrefs MIM : 130610
HGNC : HGNC
Ensembl : ENSG00000167658
HPRD : 00561
Vega : OTTHUMG00000181790
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EEF2
BioGPS: 1938
Gene Expression Atlas: ENSG00000167658
The Human Protein Atlas: ENSG00000167658
PathwayNCI Pathway Interaction Database: EEF2
KEGG: EEF2
REACTOME: EEF2
ConsensusPathDB
Pathway Commons: EEF2
MetabolismMetaCyc: EEF2
HUMANCyc: EEF2
RegulationEnsembl's Regulation: ENSG00000167658
miRBase: chr19 :3,976,053-3,985,461
TargetScan: NM_001961
cisRED: ENSG00000167658
ContextiHOP: EEF2
cancer metabolism search in PubMed: EEF2
UCL Cancer Institute: EEF2
Assigned class in ccmGDBC

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Phenotypic Information for EEF2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EEF2
Familial Cancer Database: EEF2
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EEF2
MedGen: EEF2 (Human Medical Genetics with Condition)
ClinVar: EEF2
PhenotypeMGI: EEF2 (International Mouse Phenotyping Consortium)
PhenomicDB: EEF2

Mutations for EEF2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasEEF2chr1939798563979876ITGB1BP3chr1939357913935811
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EEF2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ349979EEF2171711939799473980548EEF21653761939842233985461
BE173877EEF29761939779253977992EEF2722421939819423982305
BQ308618EEF214681939813643981418OSR26018789996181099962983
CN271708EEF212071939813833982276EEF22025411939822463982967
BF801948EEF216711939781173978172EEF2682151939793443979862
DA998089EEF212741939841613985461SLC25A10275557177967948879682608
AI075687EEF21283261939819523982344EEF23125941939772413977610
AW499012EEF211881939822983982867LRRC4B188313195103752551037650
N93529EEF2291521939760543976177F1014824713113803335113803434
BC068002EEF2116591939798173985443CSNK1D16522234178020223880206799
AW874543EEF2112651939760543976308PEX1425639311069032710690464
AA452576AP2S136175194734142547341564EEF21684681939814133982397
CD580061EEF21853001939813833981992EEF22956921939819953982967
CV392722EEF213471939800193980943SPTBN133854025468704554687249
AI905878EEF2111321939806773980927TAPBP118338647465514746771
AA706989AUP1130427475378174754188EEF23034681939819453982302
T05979EEF21571939764283976484ABHD65531135822359158252974
BE763496EEF21661939808503980915EEF2613621939763363976637
BF927334EEF222711939763403976608EEF22643231939841353984194
CN263823EEF2211131939765813976672EEF21114341939762703976591
BQ347823EEF213091939765633977339EEF23084241939764413976557
BF761203EEF2162251939765333976742EEF22223651939805523980695

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)		Stat. for Synonymous SNVs
(# total SNVs=31)
Stat. for Deletions
(# total SNVs=1)		Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:3977486-3977486p.Y730Y5
chr19:3983184-3983184p.H108H3
chr19:3979938-3979938p.A491A3
chr19:3979869-3979869p.P514P3
chr19:3982420-3982420p.I205M3
chr19:3977338-3977338p.E753V2
chr19:3984133-3984133p.?2
chr19:3978146-3978146p.R580C2
chr19:3982855-3982855p.I188V2
chr19:3979426-3979426p.I538I2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample25181 2 11 51   107 14
# mutation25171 2 11 41   97 15
nonsynonymous SNV 4 51 1 11 11   26 12
synonymous SNV2112  1    3    71 3
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:3982420p.I205M3
chr19:3978065p.T482M2
chr19:3979399p.E230K2
chr19:3982347p.R607W2
chr19:3979938p.A547A2
chr19:3979966p.A491A2
chr19:3982933p.T487T1
chr19:3979984p.Y265Y1
chr19:3982008p.V669A1
chr19:3977575p.E248K1

check002.gifOther 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

check002.gifCopy Number for EEF2 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 EEF2

check002.gifGene 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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

BTBD2,EEF1A1,EEF1A1P9,EEF1G,EEF2,EIF3L,EIF4B,
FZR1,GLTSCR2,GNB2L1,GTF2F1,IMPDH2,RPL10,RPL10A,
RPL13A,RPL3,RPL4,RPL7A,RPLP0,RPS4X,UBXN6		VPS51___IFT46,CECR5,EEF1G,EEF2,EIF3B,EXOSC5,MLST8,
NLE1,PHB2,QARS,RPL18A,RPL19,RPL29,RPL7A,
RPL8,RPS18,RPS9,SLC25A6,SMARCD2,ZNF282,ZNF581

NOA1,EEF1A1,EEF1A1P9,EEF1G,EEF2,EIF3G,EIF3L,
EIF4B,GLTSCR2,GNB2L1,HNRNPA1,HNRNPA1L2,POLL,RPL13A,
RPL28,RPL3,RPLP0,RPS15,RPS2,UBA52,ZNF581		BTBD2,NOA1,ADCK3,CIZ1,CNNM3,DYRK1B,EEF2,
EIF3D,EIF3F,EIF3L,GLTSCR2,IRF2BP1,LETMD1,PCBP2,
WDTC1,XAB2,ZNF358,ZNF395,ZNF574,ZNF579,ZNF581
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 EEF2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02059eukaryotic translation elongation factor 2experimentalAdenosine-5-Diphosphoribose
DB03223eukaryotic translation elongation factor 2experimentalDiphthamide
DB04315eukaryotic translation elongation factor 2experimentalGuanosine-5'-Diphosphate
DB08348eukaryotic translation elongation factor 2experimentalN~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
DB00877eukaryotic translation elongation factor 2approved; investigationalSirolimus


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Cross referenced IDs for EEF2
* 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



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