title: Inferring protein domains associated with drug side effects based on drug-target interaction network.
abstract: BACKGROUND
  Most phenotypic effects of drugs are involved in the interactions between drugs and their target proteins, however, our knowledge about the molecular mechanism of the drug-target interactions is very limited. One of challenging issues in recent pharmaceutical science is to identify the underlying molecular features which govern drug-target interactions.
  
  
  RESULTS
  In this paper, we make a systematic analysis of the correlation between drug side effects and protein domains, which we call "pharmacogenomic features," based on the drug-target interaction network. We detect drug side effects and protein domains that appear jointly in known drug-target interactions, which is made possible by using classifiers with sparse models. It is shown that the inferred pharmacogenomic features can be used for predicting potential drug-target interactions. We also discuss advantages and limitations of the pharmacogenomic features, compared with the chemogenomic features that are the associations between drug chemical substructures and protein domains.
  
  
  CONCLUSIONS
  The inferred side effect-domain association network is expected to be useful for estimating common drug side effects for different protein families and characteristic drug side effects for specific protein domains.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Iwata
authors.forename: Sayaka
authors.initials: S
authors.lastname: Mizutani
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Tabei
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kotera
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamanishi
mesh_terms: D019295:Computational Biology / Q000379:methods*; D064420:Drug-Related Side Effects and Adverse Reactions / Q000235:genetics / Q000378:metabolism*; D058990:Molecular Targeted Therapy; D004364:Pharmaceutical Preparations / Q000378:metabolism*; D010597:Pharmacogenetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins