mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for YARS
Gene summary
Basic gene Info.Gene symbolYARS
Gene nametyrosyl-tRNA synthetase
CytomapUCSC genome browser: 1p35.1
Type of geneprotein-coding
Descriptiontyrosine tRNA ligase 1, cytoplasmictyrosine--tRNA ligase, cytoplasmictyrosyl--tRNA ligasetyrosyl-tRNA synthetase, cytoplasmic
Modification date20141207
dbXrefs MIM : 603623
Ensembl : ENSG00000134684
HPRD : 09153
Vega : OTTHUMG00000003933
ProteinUniProt: P54577
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_YARS
BioGPS: 8565
PathwayNCI Pathway Interaction Database: YARS
Pathway Commons: YARS
ContextiHOP: YARS
ligand binding site mutation search in PubMed: YARS
UCL Cancer Institute: YARS
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for YARS

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, 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.

Protein structure related information for YARS
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for YARS from PDB

Differential gene expression and gene-gene network for YARS
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of YARS and the right PPI network was created from samples without mutations in the LBS of YARS. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for YARS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1842237Charcot-Marie-Tooth Disease, Dominant Intermediate C1Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for YARS
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|nutraceuticalDB00135L-TyrosineSmall molecule
ExperimentalDB01766Beta-(2-Naphthyl)-AlanineSmall molecule
ExperimentalDB03978TyrosinalSmall molecule
ExperimentalDB08371PARA-(BENZOYL)-PHENYLALANINESmall molecule
ExperimentalDB086174-(2,2,2-TRIFLUOROETHYL)-L-PHENYLALANINESmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of YARS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of YARS
Multiple alignments for P54577 in multiple species
LBSAA sequence# speciesSpecies
A74VTILFADLHAY7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
A74VTVLLADLHAF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A74VTVLLADVHAF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D173GLQALDEEYLK7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
D173LMQALDEQFLD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D173GMQALDEQYLG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G41LKVYWGTATTG4Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
G41LKIYWGTATTG1Homo sapiens
G41LRIYWGTATTG1Xenopus tropicalis
G41VKIYWGTATTG1Gallus gallus
G41LKLYWGTAPTG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G41ISLYWGSAPTG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H77LFADLHAYLDN7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
H77LLADLHAFLDN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H77LLADVHAFLDN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L72CEVTILFADLH7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
L72CEVTVLLADLH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L72VHVTVLLADVH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q170LYPGLQALDEE7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
Q170IYPLMQALDEQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q170IYPGMQALDEQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q182LKVDAQFGGVD5Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
Q182LKVDAQFGGID2Homo sapiens, Rattus norvegicus
Q182LDVDCQFGGVD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q182LGVDVQFGGVD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q188FGGVDQRKIFT5Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
Q188FGGIDQRKIFT2Homo sapiens, Rattus norvegicus
Q188FGGVDQRKIFV2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V152KAGAEVVKQVE7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
V152RAGADVVKQVA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V152RAGAEVVKQVA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y166LSGLLYPGLQA7Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus
Y166LSGLIYPLMQA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y166LSSLIYPGMQA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y39RELKVYWGTAT4Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
Y39RELKIYWGTAT1Homo sapiens
Y39RPLRIYWGTAT1Xenopus tropicalis
Y39REVKIYWGTAT1Gallus gallus
Y39RHLKLYWGTAP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y39RDISLYWGSAP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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