Published March 16, 2020
| Version 1.2
Dataset
Open
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (drug matrix dataset)
Authors/Creators
- 1. Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
- 2. Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada , Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- 3. Department of Toxicogenomics, GROW School of Oncology and Development Biology, Maastricht University, Maastricht, The Netherlands
- 4. Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada Ontario Institute for Cancer Research, Toronto, ON M5G 1L7, Canada Vector Institute for Artificial Intelligence, Toronto, ON M5G 1L7, Canada
Description
This data was generated by Ganter B, Snyder RD, Halbert DN, Lee MD. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics [Internet]. 2006 Oct;7(7):1025–1044. Available from: http://dx.doi.org/10.2217/14622416.7.7.1025 PMID: 17054413. The data have been curated and analyzed using our open-source R package, ToxicoGx (cran.r-project.org/web/packages/ToxicoGx) and are available publicly in the ToxicoDB web application (www.toxicodb.ca).
Notes
- Converted the expressionSet object to SummarizedExperiment
- Converted the dataset structure to match the updated version of ToxicoGx currently being submitted to Bioconductor
- Updated drug annotations in the dataset to use the most recent PubChem names
- The ToxicoGx package is being transitioned from CRAN to Biocondcutor, to access the package please run `BiocManager::install("ToxicoGx")` in your R terminal
- URL of the package in Bioconductor : http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html
Files
Files
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