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 EEF1D
Basic gene info.Gene symbolEEF1D
Gene nameeukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)
SynonymsEF-1D|EF1D|FP1047
CytomapUCSC genome browser: 8q24.3
Genomic locationchr8 :144661866-144679845
Type of geneprotein-coding
RefGenesNM_001130053.2,
NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1,
NM_001289950.1,NM_001960.4,NM_032378.4,NM_001130054.1,
Ensembl idENSG00000104529
DescriptionEF-1-deltaantigen NY-CO-4elongation factor 1-deltaguanine nucleotide exchange protein
Modification date20141207
dbXrefs MIM : 130592
HGNC : HGNC
Ensembl : ENSG00000104529
HPRD : 00560
Vega : OTTHUMG00000165191
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EEF1D
BioGPS: 1936
Gene Expression Atlas: ENSG00000104529
The Human Protein Atlas: ENSG00000104529
PathwayNCI Pathway Interaction Database: EEF1D
KEGG: EEF1D
REACTOME: EEF1D
ConsensusPathDB
Pathway Commons: EEF1D
MetabolismMetaCyc: EEF1D
HUMANCyc: EEF1D
RegulationEnsembl's Regulation: ENSG00000104529
miRBase: chr8 :144,661,866-144,679,845
TargetScan: NM_001130053
cisRED: ENSG00000104529
ContextiHOP: EEF1D
cancer metabolism search in PubMed: EEF1D
UCL Cancer Institute: EEF1D
Assigned class in ccmGDBC

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Phenotypic Information for EEF1D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EEF1D
Familial Cancer Database: EEF1D
* 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: EEF1D
MedGen: EEF1D (Human Medical Genetics with Condition)
ClinVar: EEF1D
PhenotypeMGI: EEF1D (International Mouse Phenotyping Consortium)
PhenomicDB: EEF1D

Mutations for EEF1D
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EEF1D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF513928EEF1D11558144672143144679549EEF1D1515198144671712144672080
BG004570XRN28163202131126021312271EEF1D1592838144674315144674439
BG955510EEF1D12018144662865144663465EEF1D1842498144663430144663499
DB154094EEF1D1678144679517144679583UBE2L367596222194715021976050
BQ925563PSMB716079127119210127119816EEF1D6088558144668389144679566
BF912863SORT1301431109856567109856681EEF1D1354018144662875144668431
BI860302EEF1D12958144662237144662830NFKBIB287637193939880939399159
BG545390B2M2100154500371545003812EEF1D952538144674959144675116
BC034020B2M198154500371545003812EEF1D932518144674959144675116
BC008012RPL304341589905394999057600EEF1D40713778144661898144679574
BF513932EEF1D11558144672143144679549EEF1D1514938144671738144672080

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             1   
GAIN (# sample)             1   
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)

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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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr8:144671244-144671244p.R336R7
chr8:144671685-144671685p.D189E6
chr8:144671277-144671277p.A325A2
chr8:144668984-144668984p.I377T2
chr8:144663466-144663466p.S440S2
chr8:144668985-144668985p.I377F2
chr8:144663282-144663282p.R477Q2
chr8:144663283-144663283p.R477W2
chr8:144671992-144671992p.K87fs*731
chr8:144661995-144661995p.Q637H1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample33 11    2  211  26 7
# mutation33 8    3  211  26 8
nonsynonymous SNV11 6    2  111   4 7
synonymous SNV22 2    1  1    22 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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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
chr8:144663283p.G72G,EEF1D2
chr8:144663400p.R87Q,EEF1D2
chr8:144668984p.I11T,EEF1D2
chr8:144668985p.R87W,EEF1D2
chr8:144663282p.I11V,EEF1D2
chr8:144668937p.A2A,EEF1D1
chr8:144662283p.R71C,EEF1D1
chr8:144671911p.S318G,EEF1D1
chr8:144663399p.V230V,EEF1D1
chr8:144668953p.S62G,EEF1D1

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 EEF1D 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 EEF1D

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.

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

ADCK5,ANKRD19P,ARL6IP4,C19orf70,COMMD5,CYHR1,EEF1D,
EXOSC4,GLI4,GSDMD,MAF1,NDUFA11,NDUFA13,NDUFB7,
PUF60,PYCRL,RPL8,RPS9,SHARPIN,TIMM13,VPS28
BRMS1,C12orf10,DGCR6L,EDF1,EEF1D,EIF3G,MZT2B,
FAU,MRPS26,NFKBIL1,NT5C,POLR2F,PQBP1,PRDX5,
PRPF31,RFXANK,RPS15,RUVBL2,SDHAF1,STRA13,SURF2

BOP1,HGH1,COMMD5,CYC1,CYHR1,EEF1D,EIF3E,
EIF3H,EXOSC4,GPAA1,HSF1,MAF1,NDUFB9,PUF60,
PYCRL,RPL30,RPL8,RPS20,SHARPIN,TATDN1,TOP1MT
ARL2,C10orf35,COPRS,C20orf27,FAM229B,CAMK1,COPS7A,
CUEDC2,DRAP1,EEF1D,EMD,FAM195B,IGFBP7,NDNL2,
NT5C3B,PRMT2,R3HCC1,IFT22,SELM,SNRPN,UBE2D4
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 EEF1D


There's no related Drug.
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Cross referenced IDs for EEF1D
* 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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