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ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
Sisira Kadambat Nair1, Christopher Eeles1, Chantal Ho1
1Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.
Nucleic Acids Research
|May 19, 2020
Summary
ToxicoDB is a new platform offering easy access to toxicogenomic data from in vitro studies. It aids researchers in analyzing chemical toxicity and understanding adverse outcomes.
Area of Science:
- Toxicology
- Bioinformatics
- Genomics
Background:
- Global initiatives aim to improve chemical safety testing and develop new risk assessment methods.
- Toxicogenomic profiling of mammalian cells has generated valuable datasets and analytical tools.
Purpose of the Study:
- To develop ToxicoDB, a cloud-based platform for accessing and analyzing toxicogenomic data.
- To integrate data from large in vitro toxicogenomic studies, including gene expression profiles.
Main Methods:
- Developed ToxicoDB, a free and open cloud-based platform.
- Integrated gene expression profiles of human and rat hepatocytes treated with 231 toxicants.
- Implemented harmonized chemical annotations, time- and dose-dependent plots, and pathway analysis.
Main Results:
- ToxicoDB provides streamlined access to organized, curated toxicogenomic data.
- Users can analyze compound effects across datasets and explore toxicity-related pathways.
- Data generated using the open-source R package ToxicoGx.
Conclusions:
- ToxicoDB facilitates efficient mining of complex toxicogenomic data.
- The platform supports preclinical toxicity studies and enhances understanding of adverse outcomes.
- ToxicoDB promotes accessibility and analysis of valuable toxicogenomic information.
