title: Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform.
abstract: BACKGROUND
  In early stage drug development, it is desirable to assess the toxicity of compounds as quickly as possible. Biomarker genes can help predict whether a candidate drug will adversely affect a given individual, but they are often difficult to discover. In addition, the mechanism of toxicity of many drugs and common compounds is not yet well understood. The Japanese Toxicogenomics Project provides a large database of systematically collected microarray samples from rats (liver, kidney and primary hepatocytes) and human cells (primary hepatocytes) after exposure to 170 different compounds in different dosages and at different time intervals. However, until now, no intuitive user interface has been publically available, making it time consuming and difficult for individual researchers to explore the data.
  
  
  RESULTS
  We present Toxygates, a user-friendly integrated analysis platform for this database. Toxygates combines a large microarray dataset with the ability to fetch semantic linked data, such as pathways, compound-protein interactions and orthologs, on demand. It can also perform pattern-based compound ranking with respect to the expression values of a set of relevant candidate genes. By using Toxygates, users can freely interrogate the transcriptome's response to particular compounds and conditions, which enables deep exploration of toxicity mechanisms.
authors.affiliation: National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan and Centre for Knowledge Structuring, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Johan
authors.initials: J
authors.lastname: Nyström-Persson
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Igarashi
authors.forename: Maori
authors.initials: M
authors.lastname: Ito
authors.forename: Mizuki
authors.initials: M
authors.lastname: Morita
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Nakatsu
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yamada
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000032:analysis*; D016208:Databases, Factual; D004305:Dose-Response Relationship, Drug; D005786:Gene Expression Regulation / Q000187:drug effects*; D005978:Glutathione / Q000378:metabolism; D022781:Hepatocytes / Q000187:drug effects; D006801:Humans; D007668:Kidney / Q000187:drug effects; D008099:Liver / Q000187:drug effects; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D051381:Rats; D012984:Software; D043922:Toxicogenetics; D014584:User-Computer Interface
chemical_list: D015415:Biomarkers; D005978:Glutathione