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

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 prof...

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Autores principales: Nair, Sisira Kadambat, Eeles, Christopher, Ho, Chantal, Beri, Gangesh, Yoo, Esther, Tkachuk, Denis, Tang, Amy, Nijrabi, Parwaiz, Smirnov, Petr, Seo, Heewon, Jennen, Danyel, Haibe-Kains, Benjamin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319553/
https://www.ncbi.nlm.nih.gov/pubmed/32421831
http://dx.doi.org/10.1093/nar/gkaa390
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author Nair, Sisira Kadambat
Eeles, Christopher
Ho, Chantal
Beri, Gangesh
Yoo, Esther
Tkachuk, Denis
Tang, Amy
Nijrabi, Parwaiz
Smirnov, Petr
Seo, Heewon
Jennen, Danyel
Haibe-Kains, Benjamin
author_facet Nair, Sisira Kadambat
Eeles, Christopher
Ho, Chantal
Beri, Gangesh
Yoo, Esther
Tkachuk, Denis
Tang, Amy
Nijrabi, Parwaiz
Smirnov, Petr
Seo, Heewon
Jennen, Danyel
Haibe-Kains, Benjamin
author_sort Nair, Sisira Kadambat
collection PubMed
description 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.
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spelling pubmed-73195532020-07-01 ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets Nair, Sisira Kadambat Eeles, Christopher Ho, Chantal Beri, Gangesh Yoo, Esther Tkachuk, Denis Tang, Amy Nijrabi, Parwaiz Smirnov, Petr Seo, Heewon Jennen, Danyel Haibe-Kains, Benjamin Nucleic Acids Res Web Server Issue 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. Oxford University Press 2020-07-02 2020-05-18 /pmc/articles/PMC7319553/ /pubmed/32421831 http://dx.doi.org/10.1093/nar/gkaa390 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Nair, Sisira Kadambat
Eeles, Christopher
Ho, Chantal
Beri, Gangesh
Yoo, Esther
Tkachuk, Denis
Tang, Amy
Nijrabi, Parwaiz
Smirnov, Petr
Seo, Heewon
Jennen, Danyel
Haibe-Kains, Benjamin
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title_full ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title_fullStr ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title_full_unstemmed ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title_short ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
title_sort toxicodb: an integrated database to mine and visualize large-scale toxicogenomic datasets
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319553/
https://www.ncbi.nlm.nih.gov/pubmed/32421831
http://dx.doi.org/10.1093/nar/gkaa390
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