Published March 16, 2020 | Version 1.4
Dataset Open

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

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 page links to the data associated with the publication "ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets ". The data have been curated and analyzed using our open-source R package, ToxicoGx (https://github.com/bhklab/ToxicoGx) and are available publicly in the ToxicoDB web application (www.toxicodb.ca). Please see the included DOIs below, or download the .csv file which contains the names, dates and DOIs of all datasets listed here.

The TGGATES 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.

Data:

This Drug Matrix 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.

Data:

Notes

- This file has been updated to point to two new Tsets that are DNA viability counterparts of TG-GATEs dataset. - This file has been updated to point to the new versions of TGGATES_ratldh, TGGATES_humanldh and drugMatrix_rat - These tSets are now available using the downloadTSet function in the ToxicoGx pacakge; please see included documentation for usage instructions - This data is idententical to the last release but has updapted tSet DOIs and an appropriate version bump

Files

availableTSets.csv

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