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 EARS2
Basic gene info.Gene symbolEARS2
Gene nameglutamyl-tRNA synthetase 2, mitochondrial
SynonymsCOXPD12|MSE1
CytomapUCSC genome browser: 16p12.2
Genomic locationchr16 :23533333-23568696
Type of geneprotein-coding
RefGenesNM_001083614.1,
NR_003501.1,
Ensembl idENSG00000103356
DescriptiongluRSglutamate tRNA ligase 2, mitochondrialglutamate--tRNA ligaseglutamyl-tRNA synthetase 2, mitochondrial (putative)probable glutamate--tRNA ligase, mitochondrialprobable glutamyl-tRNA synthetase, mitochondrial
Modification date20141207
dbXrefs MIM : 612799
HGNC : HGNC
Ensembl : ENSG00000103356
Vega : OTTHUMG00000177018
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EARS2
BioGPS: 124454
Gene Expression Atlas: ENSG00000103356
The Human Protein Atlas: ENSG00000103356
PathwayNCI Pathway Interaction Database: EARS2
KEGG: EARS2
REACTOME: EARS2
ConsensusPathDB
Pathway Commons: EARS2
MetabolismMetaCyc: EARS2
HUMANCyc: EARS2
RegulationEnsembl's Regulation: ENSG00000103356
miRBase: chr16 :23,533,333-23,568,696
TargetScan: NM_001083614
cisRED: ENSG00000103356
ContextiHOP: EARS2
cancer metabolism search in PubMed: EARS2
UCL Cancer Institute: EARS2
Assigned class in ccmGDBC

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Phenotypic Information for EARS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EARS2
Familial Cancer Database: EARS2
* 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: EARS2
MedGen: EARS2 (Human Medical Genetics with Condition)
ClinVar: EARS2
PhenotypeMGI: EARS2 (International Mouse Phenotyping Consortium)
PhenomicDB: EARS2

Mutations for EARS2
* 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 EARS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW605160HMGB284654174253196174254307EARS2453561162353543123535539

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)                 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr16:23555840-23555840p.T160T2
chr16:23546599-23546599p.R190C2
chr16:23546255-23546255p.P304P1
chr16:23535757-23535757p.E503Q1
chr16:23563572-23563572p.K65*1
chr16:23541078-23541078p.L403P1
chr16:23546257-23546257p.P304S1
chr16:23536559-23536559p.?1
chr16:23555844-23555844p.Q159R1
chr16:23563615-23563615p.H50H1

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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
# sample13 3  21 1 43  1 6 5
# mutation13 3  21 1 43  1 6 6
nonsynonymous SNV13 2  1    33    3 5
synonymous SNV   1  11 1 1   1 3 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
chr16:23546599p.R190C2
chr16:23541092p.E503Q1
chr16:23546671p.D216G1
chr16:23535745p.R489W1
chr16:23543988p.L201M1
chr16:23555840p.V449V1
chr16:23535757p.D200N1
chr16:23546255p.V444A1
chr16:23555867p.A429V1
chr16:23536588p.R166W1

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 EARS2 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 EARS2

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

ALG1,FOPNL,KNOP1,COG7,COQ7,DNAJA3,EARS2,
ERI2,GLYR1,GSPT1,HN1L,PARN,POLR3E,RRN3,
THUMPD1,UBFD1,USP7,ZKSCAN2,ZNF174,ZNF263,ZSCAN32
BEND3,C10orf2,COBL,DAG1,DKC1,EARS2,GLB1L2,
IPO4,KIAA1324,LARS,LIG3,MANEAL,MCM4,PAICS,
PDCD11,PLCH1,PLEKHH1,POLR1B,SLC12A8,UCK2,WWC1

KNOP1,CCDC86,DHODH,DNAJA3,DPH2,EARS2,EEF2KMT,
GOT2,GSPT1,HN1L,NUP93,PALB2,PDF,PLK1,
POLR3E,RNF40,TMEM186,TRAP1,TUFM,UBFD1,XPO6
ABCE1,ACAD9,DDX10,DDX56,DHODH,DKC1,EARS2,
FARSB,KIAA0020,NOP14,PAICS,PPIF,PRMT5,PRPF4,
PUS1,PUS7,RRP9,SRFBP1,UTP14A,WDR3,WDR77
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 EARS2
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-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Glutamic Acid
DB00145glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalGlycine
DB00160glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Alanine
DB00125glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Arginine
DB00151glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Cysteine
DB00130glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceutical; investigationalL-Glutamine
DB00117glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Histidine
DB00149glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Leucine
DB00123glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Lysine
DB00134glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Methionine
DB00120glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Phenylalanine
DB00133glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Serine
DB00156glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Threonine
DB00150glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Tryptophan
DB00135glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Tyrosine
DB00161glutamyl-tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Valine


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Cross referenced IDs for EARS2
* 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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