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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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. |
format | Online Article Text |
id | pubmed-7319553 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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