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 EPRS
Basic gene info.Gene symbolEPRS
Gene nameglutamyl-prolyl-tRNA synthetase
SynonymsEARS|GLUPRORS|PARS|QARS|QPRS
CytomapUCSC genome browser: 1q41
Genomic locationchr1 :220141941-220220000
Type of geneprotein-coding
RefGenesNM_004446.2,
Ensembl idENSG00000136628
Descriptionbifunctional aminoacyl-tRNA synthetasebifunctional glutamate/proline--tRNA ligasecell proliferation-inducing gene 32 proteinglutamate tRNA ligaseglutamatyl-prolyl-tRNA synthetaseglutaminyl-tRNA synthetaseproliferation-inducing gene 32 proteinprolif
Modification date20141207
dbXrefs MIM : 138295
HGNC : HGNC
Ensembl : ENSG00000136628
HPRD : 00703
Vega : OTTHUMG00000037433
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EPRS
BioGPS: 2058
Gene Expression Atlas: ENSG00000136628
The Human Protein Atlas: ENSG00000136628
PathwayNCI Pathway Interaction Database: EPRS
KEGG: EPRS
REACTOME: EPRS
ConsensusPathDB
Pathway Commons: EPRS
MetabolismMetaCyc: EPRS
HUMANCyc: EPRS
RegulationEnsembl's Regulation: ENSG00000136628
miRBase: chr1 :220,141,941-220,220,000
TargetScan: NM_004446
cisRED: ENSG00000136628
ContextiHOP: EPRS
cancer metabolism search in PubMed: EPRS
UCL Cancer Institute: EPRS
Assigned class in ccmGDBC

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

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

Mutations for EPRS
* 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 EPRS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample7  2  1 2 1      
GAIN (# sample)7  2  1 1 1      
LOSS (# sample)        1        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=120)
Stat. for Synonymous SNVs
(# total SNVs=26)
Stat. for Deletions
(# total SNVs=6)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:220151974-220151974p.R1333*3
chr1:220142172-220142172p.Y1505Y3
chr1:220208271-220208271p.L72L2
chr1:220170392-220170392p.S825Y2
chr1:220197801-220197801p.?2
chr1:220170408-220170408p.I820L2
chr1:220174484-220174484p.N726fs*152
chr1:220156704-220156704p.I1043V2
chr1:220146601-220146601p.I1408T2
chr1:220156132-220156132p.R1119C2

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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
# sample43 182 3 5  16102 11111121
# mutation43 212 3 5  21122 11112127
nonsynonymous SNV33 202 2 3  20121 187116
synonymous SNV1  1  1 2  1 1  35 11
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
chr1:220146601p.S825F2
chr1:220170392p.D762N2
chr1:220191809p.R358H2
chr1:220208271p.I492I2
chr1:220170582p.G329W2
chr1:220195731p.L72L2
chr1:220195819p.I1408T2
chr1:220160638p.G676G1
chr1:220184292p.W450L1
chr1:220205767p.L1335I1

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 EPRS 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 EPRS

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

ACBD3,AHCTF1,BPNT1,DIEXF,SPRTN,BROX,EPRS,
FBXO28,HEATR1,IARS2,LIN9,NUP133,DESI2,RAB3GAP2,
RRP15,TAF1A,TAF5L,TFB2M,UCHL5,URB2,ZNF124
TRAPPC11,CKAP5,CSNK2A3,DYM,EPRS,IARS,IPO7,
NLN,NUP155,OSBP,PCM1,POLR2B,PRKDC,SKIV2L2,
TTC37,TUBGCP4,UCHL5,USP7,YME1L1,ZFR,ZRANB3

ADSS,AHCTF1,ATF6,DIEXF,COG2,EPRS,FBXO28,
FH,GABPB2,HEATR1,IARS2,IPO9,KIAA1804,NDUFS2,
NUP133,PPP1R15B,RAB4A,RBBP5,TAF5L,TTC13,URB2
AQR,ASCC3,BMS1,DDX46,DHX9,EIF4G1,EPRS,
HNRNPK,HNRNPU,IDE,FOCAD,KPNB1,NRD1,PRKDC,
PSME4,SF3B3,TRIP12,UGGT1,VCP,VPRBP,XPO5
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 EPRS
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
DB00142glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Glutamic Acid
DB00172glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Proline
DB02510glutamyl-prolyl-tRNA synthetaseexperimental'5'-O-(N-(L-Prolyl)-Sulfamoyl)Adenosine
DB02684glutamyl-prolyl-tRNA synthetaseexperimental5'-O-(N-(L-Cysteinyl)-Sulfamoyl)Adenosine
DB03376glutamyl-prolyl-tRNA synthetaseexperimental'5'-O-(N-(L-Alanyl)-Sulfamoyl)Adenosine
DB00145glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalGlycine
DB00160glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Alanine
DB00125glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Arginine
DB00151glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Cysteine
DB00130glutamyl-prolyl-tRNA synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00117glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Histidine
DB00149glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Leucine
DB00123glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Lysine
DB00134glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Methionine
DB00120glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Phenylalanine
DB00133glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Serine
DB00156glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Threonine
DB00150glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Tryptophan
DB00135glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Tyrosine
DB00161glutamyl-prolyl-tRNA synthetaseapproved; nutraceuticalL-Valine


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Cross referenced IDs for EPRS
* 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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