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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for WARS |
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Phenotypic Information for WARS(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: WARS |
Familial Cancer Database: WARS |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_TRYPTOPHAN_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: WARS |
MedGen: WARS (Human Medical Genetics with Condition) | |
ClinVar: WARS | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | WARS | chr14 | 100840200 | 100840220 | chr14 | 100685879 | 100685899 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows WARS related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BF988254 | GADD45G | 13 | 97 | 9 | 92219927 | 92220011 | WARS | 92 | 225 | 14 | 100803470 | 100808798 | |
BM977906 | MARK3 | 18 | 447 | 14 | 103964837 | 103969619 | WARS | 446 | 588 | 14 | 100835424 | 100835566 | |
T63251 | WARS | 3 | 180 | 14 | 100801169 | 100801348 | WARS | 176 | 263 | 14 | 100801062 | 100801149 | |
AI268655 | WARS | 10 | 63 | 14 | 100801073 | 100801126 | WARS | 58 | 427 | 14 | 100800717 | 100801086 | |
AW794469 | ZNF695 | 191 | 228 | 1 | 247163785 | 247163822 | WARS | 211 | 539 | 14 | 100817444 | 100817841 | |
AW796806 | WARS | 6 | 67 | 14 | 100800943 | 100801004 | WARS | 60 | 143 | 14 | 100800860 | 100800943 | |
S74703 | WARS | 1 | 450 | 14 | 100800854 | 100801304 | NFYC | 448 | 1862 | 1 | 41218892 | 41237273 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=33) | (# total SNVs=10) |
(# total SNVs=0) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr14:100808747-100808747 | p.Q367H | 2 |
chr14:100801346-100801346 | p.G428S | 2 |
chr14:100828143-100828143 | p.N72S | 2 |
chr14:100828181-100828181 | p.K59K | 2 |
chr14:100826957-100826957 | p.R119L | 2 |
chr14:100809692-100809692 | p.P287S | 1 |
chr14:100835456-100835456 | p.V23I | 1 |
chr14:100801263-100801263 | p.E455D | 1 |
chr14:100820169-100820169 | p.Q194* | 1 |
chr14:100803478-100803478 | p.G392V | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   | 1 | 5 | 1 |   |   |   | 2 |   |   | 5 | 5 | 1 |   |   | 5 | 4 |   | 7 |
# mutation |   |   | 1 | 5 | 1 |   |   |   | 2 |   |   | 5 | 6 | 1 |   |   | 5 | 3 |   | 7 |
nonsynonymous SNV |   |   | 1 | 4 | 1 |   |   |   |   |   |   | 4 | 4 | 1 |   |   | 4 | 2 |   | 6 |
synonymous SNV |   |   |   | 1 |   |   |   |   | 2 |   |   | 1 | 2 |   |   |   | 1 | 1 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr14:100808747 | p.G387S,WARS | 2 |
chr14:100801346 | p.Q326H,WARS | 2 |
chr14:100820164 | p.T412A,WARS | 1 |
chr14:100801237 | p.I225M,WARS | 1 |
chr14:100828197 | p.Y9C,WARS | 1 |
chr14:100820787 | p.V411I,WARS | 1 |
chr14:100801271 | p.F219L,WARS | 1 |
chr14:100828209 | p.V23I,WARS | 1 |
chr14:100808790 | p.V396V,WARS | 1 |
chr14:100820803 | p.G201R,WARS | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for WARS |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00150 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Tryptophan | ||
DB01831 | tryptophanyl-tRNA synthetase | experimental | Tryptophanyl-5'amp | ||
DB04537 | tryptophanyl-tRNA synthetase | experimental | L-Tryptophanamide | ||
DB00145 | tryptophanyl-tRNA synthetase | approved; nutraceutical | Glycine | ||
DB00160 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Alanine | ||
DB00125 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Arginine | ||
DB00151 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Cysteine | ||
DB00130 | tryptophanyl-tRNA synthetase | approved; nutraceutical; investigational | L-Glutamine | ||
DB00117 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Histidine | ||
DB00149 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Leucine | ||
DB00123 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Lysine | ||
DB00134 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Methionine | ||
DB00120 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Phenylalanine | ||
DB00172 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Proline | ||
DB00133 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Serine | ||
DB00156 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Threonine | ||
DB00135 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-Tyrosine | ||
DB00161 | tryptophanyl-tRNA synthetase | approved; nutraceutical | L-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 |
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