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 WARS2
Basic gene info.Gene symbolWARS2
Gene nametryptophanyl tRNA synthetase 2, mitochondrial
SynonymsTrpRS
CytomapUCSC genome browser: 1p12
Genomic locationchr1 :119573838-119683295
Type of geneprotein-coding
RefGenesNM_015836.3,
NM_201263.2,
Ensembl idENSG00000116874
Description(Mt)TrpRStryptophan tRNA ligase 2, mitochondrialtryptophan--tRNA ligase, mitochondrialtryptophan-tRNA ligasetryptophanyl-tRNA synthetase, mitochondrial
Modification date20141207
dbXrefs MIM : 604733
HGNC : HGNC
Ensembl : ENSG00000116874
HPRD : 05295
Vega : OTTHUMG00000012335
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WARS2
BioGPS: 10352
Gene Expression Atlas: ENSG00000116874
The Human Protein Atlas: ENSG00000116874
PathwayNCI Pathway Interaction Database: WARS2
KEGG: WARS2
REACTOME: WARS2
ConsensusPathDB
Pathway Commons: WARS2
MetabolismMetaCyc: WARS2
HUMANCyc: WARS2
RegulationEnsembl's Regulation: ENSG00000116874
miRBase: chr1 :119,573,838-119,683,295
TargetScan: NM_015836
cisRED: ENSG00000116874
ContextiHOP: WARS2
cancer metabolism search in PubMed: WARS2
UCL Cancer Institute: WARS2
Assigned class in ccmGDBC

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Phenotypic Information for WARS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: WARS2
Familial Cancer Database: WARS2
* 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_TRYPTOPHAN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: WARS2
MedGen: WARS2 (Human Medical Genetics with Condition)
ClinVar: WARS2
PhenotypeMGI: WARS2 (International Mouse Phenotyping Consortium)
PhenomicDB: WARS2

Mutations for WARS2
* 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
pancreasWARS2chr1119624293119624313WARS2chr1119619393119619413
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 WARS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI672033VAV313351108417521108507503WARS23324591119584927119588287
AK294729WARS214031119683014119683416RYR240113091237850752237872179
DA579087WARS232391119683040119683276LOXL224058082319098323198691
DC320785WARS214031119683014119683416RYR24015571237850752237863571

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 # sample5         1      
GAIN (# sample)5         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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr1:119576827-119576827p.H175H2
chr1:119584928-119584928p.L158L2
chr1:119619117-119619117p.S68S2
chr1:119619004-119619004p.P106L1
chr1:119619219-119619219p.K34N1
chr1:119619015-119619015p.C102C1
chr1:119683216-119683216p.A18T1
chr1:119576834-119576834p.S173F1
chr1:119619051-119619051p.Q90H1
chr1:119683237-119683237p.E11*1

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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
# sample   11  4 3  631 169 4
# mutation   10  4 3  1131 169 4
nonsynonymous SNV   7  4 2  821  47 3
synonymous SNV   3    1  31  122 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
chr1:119575743p.R292C2
chr1:119575670p.P316R2
chr1:119619097p.D75G,WARS22
chr1:119575732p.A295A2
chr1:119619197p.R36L,WARS21
chr1:119575735p.R292H1
chr1:119575905p.Q194L,WARS21
chr1:119584944p.K34N,WARS21
chr1:119575586p.V353M1
chr1:119619214p.D181D,WARS21

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 WARS2 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 WARS2

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

ATP1A1,BPI,ATP1A1-AS1,CD58,CNTN6,CTNND1,GDAP2,
IGSF3,MDGA2,NCALD,NOTCH2,PHGDH,SEC22B,SLC39A12,
SLC43A3,SPON1,STAC2,VTCN1,WARS2,WDR3,ZNF697
AASDHPPT,C11orf57,URI1,TMA16,CNOT7,DARS,EIF2A,
EIF2S3,EIF3E,MAT2B,MBLAC2,NUP54,POC1B,RSL24D1,
TMEM69,TRMT5,WARS2,ZCCHC7,ZFAND1,ZNF22,ZNF277

ATP5F1,ATPAF2,C1QBP,CCBL2,COX5A,DPH5,LAMTOR5,
MMACHC,MRPL1,MRPL37,MRPL44,MRPS27,OXSM,PCCB,
PPA2,RPL5,SERBP1,TTC19,TXN2,UQCRH,WARS2
ADH1C,AGPAT5,ALDH3A1,ALDH7A1,MPLKIP,DTWD2,LRPPRC,
MARS2,MRPS30,NDUFA10,PCCA,PIGU,PTDSS1,PTGER2,
RNMTL1,RPIA,SEH1L,SERPINA6,SHQ1,TGIF1,WARS2
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 WARS2
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
DB00150tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Tryptophan
DB00145tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalGlycine
DB00160tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Alanine
DB00125tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Arginine
DB00151tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Cysteine
DB00130tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceutical; investigationalL-Glutamine
DB00117tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Histidine
DB00149tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Leucine
DB00123tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Lysine
DB00134tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Methionine
DB00120tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Phenylalanine
DB00133tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Serine
DB00156tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Threonine
DB00135tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Tyrosine
DB00161tryptophanyl tRNA synthetase 2, mitochondrialapproved; nutraceuticalL-Valine


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Cross referenced IDs for WARS2
* 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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