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ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets.


ABSTRACT: In the past few decades, major initiatives have been launched around the world to address chemical safety testing. These efforts aim to innovate and improve the efficacy of existing methods with the long-term goal of developing new risk assessment paradigms. The transcriptomic and toxicological profiling of mammalian cells has resulted in the creation of multiple toxicogenomic datasets and corresponding tools for analysis. To enable easy access and analysis of these valuable toxicogenomic data, we have developed ToxicoDB (toxicodb.ca), a free and open cloud-based platform integrating data from large in vitro toxicogenomic studies, including gene expression profiles of primary human and rat hepatocytes treated with 231 potential toxicants. To efficiently mine these complex toxicogenomic data, ToxicoDB provides users with harmonized chemical annotations, time- and dose-dependent plots of compounds across datasets, as well as the toxicity-related pathway analysis. The data in ToxicoDB have been generated using our open-source R package, ToxicoGx (github.com/bhklab/ToxicoGx). Altogether, ToxicoDB provides a streamlined process for mining highly organized, curated, and accessible toxicogenomic data that can be ultimately applied to preclinical toxicity studies and further our understanding of adverse outcomes.

SUBMITTER: Nair SK 

PROVIDER: S-EPMC7319553 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets.

Nair Sisira Kadambat SK   Eeles Christopher C   Ho Chantal C   Beri Gangesh G   Yoo Esther E   Tkachuk Denis D   Tang Amy A   Nijrabi Parwaiz P   Smirnov Petr P   Seo Heewon H   Jennen Danyel D   Haibe-Kains Benjamin B  

Nucleic acids research 20200701 W1


In the past few decades, major initiatives have been launched around the world to address chemical safety testing. These efforts aim to innovate and improve the efficacy of existing methods with the long-term goal of developing new risk assessment paradigms. The transcriptomic and toxicological profiling of mammalian cells has resulted in the creation of multiple toxicogenomic datasets and corresponding tools for analysis. To enable easy access and analysis of these valuable toxicogenomic data,  ...[more]

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