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Published March 16, 2020 | Version 1.2
Dataset Open

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs human 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 Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023. The data have been curated and analyzed using our open-source R package, ToxicoGx (http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html), and are available publicly in the ToxicoDB web application (www.toxicodb.ca).

Notes

- This TSet includes the LDH counterpart viability measurements. - 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 package can be accessed via Bioconductor : https://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html OR run `devtools::install_github("bhklab/ToxicoGx")` in your R terminal

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