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 ETF1
Basic gene info.Gene symbolETF1
Gene nameeukaryotic translation termination factor 1
SynonymsD5S1995|ERF|ERF1|RF1|SUP45L1|TB3-1
CytomapUCSC genome browser: 5q31.1
Genomic locationchr5 :137841781-137878989
Type of geneprotein-coding
RefGenesNM_001256302.1,
NM_001282185.1,NM_001291974.1,NM_001291975.1,NM_004730.3,
Ensembl idENSG00000120705
Descriptioneukaryotic peptide chain release factor subunit 1polypeptide chain release factor 1protein Cl1sup45 (yeast omnipotent suppressor 45) homolog-like 1
Modification date20141207
dbXrefs MIM : 600285
HGNC : HGNC
Ensembl : ENSG00000120705
HPRD : 02616
Vega : OTTHUMG00000129199
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ETF1
BioGPS: 2107
Gene Expression Atlas: ENSG00000120705
The Human Protein Atlas: ENSG00000120705
PathwayNCI Pathway Interaction Database: ETF1
KEGG: ETF1
REACTOME: ETF1
ConsensusPathDB
Pathway Commons: ETF1
MetabolismMetaCyc: ETF1
HUMANCyc: ETF1
RegulationEnsembl's Regulation: ENSG00000120705
miRBase: chr5 :137,841,781-137,878,989
TargetScan: NM_001256302
cisRED: ENSG00000120705
ContextiHOP: ETF1
cancer metabolism search in PubMed: ETF1
UCL Cancer Institute: ETF1
Assigned class in ccmGDBC

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Phenotypic Information for ETF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ETF1
Familial Cancer Database: ETF1
* 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
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ETF1
MedGen: ETF1 (Human Medical Genetics with Condition)
ClinVar: ETF1
PhenotypeMGI: ETF1 (International Mouse Phenotyping Consortium)
PhenomicDB: ETF1

Mutations for ETF1
* 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
pancreasETF1chr5137850104137850124ETF1chr5137850276137850296
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 ETF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG534374HLA-E2256617895791789963ETF12496215137846830137848637
DB041334LOC1005074121148?112032112179ETF11494475137854497137878920

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=31)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr5:137854398-137854398p.L82P4
chr5:137846256-137846256p.E361Q2
chr5:137846839-137846839p.V305I2
chr5:137853275-137853275p.L126S2
chr5:137854434-137854434p.S70L1
chr5:137848455-137848455p.Q244*1
chr5:137844008-137844008p.L434F1
chr5:137853276-137853276p.L126L1
chr5:137846286-137846286p.E351*1
chr5:137854525-137854525p.P40S1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 152 2 1 1 22  3516
# mutation21 122 2 1 1 22  3517
nonsynonymous SNV21 9  2 1 1 21  2316
synonymous SNV   32        1  12 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
chr5:137854398p.L68P,ETF14
chr5:137846839p.E347Q,ETF12
chr5:137853275p.L112S,ETF12
chr5:137846256p.V291I,ETF12
chr5:137846306p.L420F,ETF11
chr5:137848611p.N263N,ETF11
chr5:137844008p.L68L,ETF11
chr5:137854397p.F417F,ETF11
chr5:137849377p.E255Q,ETF11
chr5:137844015p.E416E,ETF11

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 ETF1 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 ETF1

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

AFF4,CDC23,CLINT1,CSNK1A1,DDX46,ETF1,FBXW11,
G3BP1,GRPEL2,HSPA4,HSPA9,LARS,MATR3,PHAX,
RARS,RBM27,SEC24A,SRFBP1,UTP15,WDR36,YIPF5
AKIRIN1,BAG5,DTD2,MIR22HG,AAED1,CDV3,DCTN6,
DEGS1,DNAJC25,DPH3,EIF2S1,ETF1,HAUS2,MAPRE1,
PPP2CB,PWP1,RNF11,SBDSP1,STRAP,UBQLN1,YWHAZ

CDC23,CSNK1A1,ETF1,G3BP1,HARS,HDAC3,HSPA4,
HSPA9,IPO11,MRPS27,NPM1,PPP2CA,RARS,RBM27,
RIOK2,SLC30A5,TMEM161B,UBE2D2,UTP15,VDAC1,WDR36
AEN,CD55,DDX21,DNTTIP2,DPY19L1,EIF3J,ETF1,
GNL2,GPATCH4,GTPBP4,IBTK,NAA50,NOL10,ODC1,
PIGW,PSMD12,PSME3,RRS1,SERPINB8,SLC25A32,UBQLN1
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 ETF1


There's no related Drug.
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Cross referenced IDs for ETF1
* 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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