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 journalArticle

123 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 languageEnglish
Pages (from-to)D921-D927
JournalNucleic Acids Research
Volume43
Issue numberD1
DOIs
Publication statusPublished - Jan 28 2015
Externally publishedYes

Fingerprint

Toxicogenetics
Genomics
Databases
Transcriptome
Safety
Animal Structures
Gene Expression
Drug Evaluation
Pharmaceutical Preparations
Toxicology
Biomarkers
Pathology

ASJC Scopus subject areas

  • Genetics

Cite this

Igarashi, Y., Nakatsu, N., Yamashita, T., Ono, A., Ohno, Y., Urushidani, T., & Yamada, H. (2015). Open TG-GATEs: A large-scale toxicogenomics database. Nucleic Acids Research, 43(D1), D921-D927. https://doi.org/10.1093/nar/gku955

Open TG-GATEs : A large-scale toxicogenomics database. / Igarashi, Yoshinobu; Nakatsu, Noriyuki; Yamashita, Tomoya; Ono, Atsushi; Ohno, Yasuo; Urushidani, Tetsuro; Yamada, Hiroshi.

In: Nucleic Acids Research, Vol. 43, No. D1, 28.01.2015, p. D921-D927.

Research output: Contribution to journalArticle

Igarashi, Y, Nakatsu, N, Yamashita, T, Ono, A, Ohno, Y, Urushidani, T & Yamada, H 2015, 'Open TG-GATEs: A large-scale toxicogenomics database', Nucleic Acids Research, vol. 43, no. D1, pp. D921-D927. https://doi.org/10.1093/nar/gku955
Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T et al. Open TG-GATEs: A large-scale toxicogenomics database. Nucleic Acids Research. 2015 Jan 28;43(D1):D921-D927. https://doi.org/10.1093/nar/gku955
Igarashi, Yoshinobu ; Nakatsu, Noriyuki ; Yamashita, Tomoya ; Ono, Atsushi ; Ohno, Yasuo ; Urushidani, Tetsuro ; Yamada, Hiroshi. / Open TG-GATEs : A large-scale toxicogenomics database. In: Nucleic Acids Research. 2015 ; Vol. 43, No. D1. pp. D921-D927.
@article{b034ca7eef2f4c809435c5175f5ffb97,
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.",
author = "Yoshinobu Igarashi and Noriyuki Nakatsu and Tomoya Yamashita and Atsushi Ono and Yasuo Ohno and Tetsuro Urushidani and Hiroshi Yamada",
year = "2015",
month = "1",
day = "28",
doi = "10.1093/nar/gku955",
language = "English",
volume = "43",
pages = "D921--D927",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

TY - JOUR

T1 - Open TG-GATEs

T2 - A large-scale toxicogenomics database

AU - Igarashi, Yoshinobu

AU - Nakatsu, Noriyuki

AU - Yamashita, Tomoya

AU - Ono, Atsushi

AU - Ohno, Yasuo

AU - Urushidani, Tetsuro

AU - Yamada, Hiroshi

PY - 2015/1/28

Y1 - 2015/1/28

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84941087170&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84941087170&partnerID=8YFLogxK

U2 - 10.1093/nar/gku955

DO - 10.1093/nar/gku955

M3 - Article

VL - 43

SP - D921-D927

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -