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 WARS
Basic gene info.Gene symbolWARS
Gene nametryptophanyl-tRNA synthetase
SynonymsGAMMA-2|IFI53|IFP53
CytomapUCSC genome browser: 14q32.31
Genomic locationchr14 :100800124-100842680
Type of geneprotein-coding
RefGenesNM_004184.3,
NM_173701.1,NM_213645.1,NM_213646.1,
Ensembl idENSG00000140105
DescriptionhWRSinterferon-induced protein 53trpRStryptophan tRNA ligase 1, cytoplasmictryptophan--tRNA ligase, cytoplasmic
Modification date20141207
dbXrefs MIM : 191050
HGNC : HGNC
Ensembl : ENSG00000140105
HPRD : 01845
Vega : OTTHUMG00000171572
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WARS
BioGPS: 7453
Gene Expression Atlas: ENSG00000140105
The Human Protein Atlas: ENSG00000140105
PathwayNCI Pathway Interaction Database: WARS
KEGG: WARS
REACTOME: WARS
ConsensusPathDB
Pathway Commons: WARS
MetabolismMetaCyc: WARS
HUMANCyc: WARS
RegulationEnsembl's Regulation: ENSG00000140105
miRBase: chr14 :100,800,124-100,842,680
TargetScan: NM_004184
cisRED: ENSG00000140105
ContextiHOP: WARS
cancer metabolism search in PubMed: WARS
UCL Cancer Institute: WARS
Assigned class in ccmGDBC

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

Mutations for WARS
* 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
ovaryWARSchr14100840200100840220chr14100685879100685899
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 WARS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF988254GADD45G139799221992792220011WARS9222514100803470100808798
BM977906MARK31844714103964837103969619WARS44658814100835424100835566
T63251WARS318014100801169100801348WARS17626314100801062100801149
AI268655WARS106314100801073100801126WARS5842714100800717100801086
AW794469ZNF6951912281247163785247163822WARS21153914100817444100817841
AW796806WARS66714100800943100801004WARS6014314100800860100800943
S74703WARS145014100800854100801304NFYC448186214121889241237273

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr14:100808747-100808747p.Q367H2
chr14:100801346-100801346p.G428S2
chr14:100828143-100828143p.N72S2
chr14:100828181-100828181p.K59K2
chr14:100826957-100826957p.R119L2
chr14:100809692-100809692p.P287S1
chr14:100835456-100835456p.V23I1
chr14:100820169-100820169p.Q194*1
chr14:100801263-100801263p.E455D1
chr14:100803478-100803478p.G392V1

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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
# sample  151   2  551  54 7
# mutation  151   2  561  53 7
nonsynonymous SNV  141      441  42 6
synonymous SNV   1    2  12   11 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
chr14:100808747p.G387S,WARS2
chr14:100801346p.Q326H,WARS2
chr14:100820164p.A244A,WARS1
chr14:100828197p.A13V,WARS1
chr14:100801237p.R423L,WARS1
chr14:100820787p.I225M,WARS1
chr14:100828209p.Y9C,WARS1
chr14:100801271p.T412A,WARS1
chr14:100808790p.F219L,WARS1
chr14:100820803p.V23I,WARS1

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 WARS 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 WARS

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 WARS
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 synthetaseapproved; nutraceuticalL-Tryptophan
DB01831tryptophanyl-tRNA synthetaseexperimentalTryptophanyl-5'amp
DB04537tryptophanyl-tRNA synthetaseexperimentalL-Tryptophanamide
DB00145tryptophanyl-tRNA synthetaseapproved; nutraceuticalGlycine
DB00160tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Alanine
DB00125tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Arginine
DB00151tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Cysteine
DB00130tryptophanyl-tRNA synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00117tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Histidine
DB00149tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Leucine
DB00123tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Lysine
DB00134tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Methionine
DB00120tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Phenylalanine
DB00172tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Proline
DB00133tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Serine
DB00156tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Threonine
DB00135tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Tyrosine
DB00161tryptophanyl-tRNA synthetaseapproved; nutraceuticalL-Valine


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Cross referenced IDs for WARS
* 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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