Open TG-GATEs: A large-scale toxicogenomics database

Yoshinobu Igarashi; Noriyuki Nakatsu; Tomoya Yamashita; Atsushi Ono; Yasuo Ohno; Tetsuro Urushidani; Hiroshi Yamada

doi:10.1093/nar/gku955

Open TG-GATEs: A large-scale toxicogenomics database

Yoshinobu Igarashi, Noriyuki Nakatsu, Tomoya Yamashita, Atsushi Ono, Yasuo Ohno, Tetsuro Urushidani, Hiroshi Yamada

Research output: Contribution to journal › Article › peer-review

291 Citations (Scopus)

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.

Original language	English
Pages (from-to)	D921-D927
Journal	Nucleic acids research
Volume	43
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gku955
Publication status	Published - Jan 28 2015
Externally published	Yes

ASJC Scopus subject areas

Genetics

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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.",

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AU - Ohno, Yasuo

AU - Urushidani, Tetsuro

AU - Yamada, Hiroshi

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Open TG-GATEs: A large-scale toxicogenomics database

Abstract

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