title: Open TG-GATEs: a large-scale toxicogenomics database.
abstract: Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological mechanisms in animal target organs. Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment. Most of the data generated by the project (e.g. gene expression, pathology, lot number) are freely available to the public via Open TG-GATEs (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System). Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database. Open TG-GATEs is available from http://toxico.nibio.go.jp/english/index.html.
authors.affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan.
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Igarashi
authors.affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Nakatsu
authors.affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan Hitachi, Ltd. Information & Telecommunication Systems Company, Government & Public Corporation Information Systems Division, Tokyo 136-8832, Japan.
authors.forename: Tomoya
authors.initials: T
authors.lastname: Yamashita
authors.affiliation: National Institute of Health and Sciences, Tokyo 158-0098, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Ono
authors.affiliation: National Institute of Health and Sciences, Tokyo 158-0098, Japan.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Ohno
authors.affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan Department of Pathophysiology, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto 610-0332, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Urushidani
authors.affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan h-yamada@nibio.go.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yamada
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D020407:Internet; D007668:Kidney / Q000187:drug effects / Q000378:metabolism / Q000473:pathology; D008099:Liver / Q000187:drug effects / Q000378:metabolism / Q000473:pathology; D008297:Male; D051381:Rats; D017207:Rats, Sprague-Dawley; D043922:Toxicogenetics; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D015415:Biomarkers