ToxAnalyzer is a webtool for analyzing compounds that provides an organized overview of the complete compound data available in the CTD database. ToxAnalyzer was developed to aid users in possible toxicogenomic studies provinding a user-friendly interface.
Frequently Asked Questions
- 1 – What is ToxAnalyzer?
- ToxAnalyzer is a webtool which aims to provide, in a single page, a detailed overview on the toxicogenomic information about chemicals, by showing information on chemical-gene interactions, organisms, types of interactions and supporting publications of those interactions and interaction types.
- 2 – What are the sources of information ToxAnalyzer pulls data from?
- ToxAnalyzer retrives its data mainly from the Comparative Toxicogenomics Database (CTD), these data are then processed to be displayed on the webpage. ToxAnalyzer links to other online resources, namely the NCBI Gene and Taxonomy databases, PubChem and PubMed.
- 3 – Why not just use CTD then, since you pull information from their database?
- A lot of manual data manipulation would be required from the user to achieve similar results to those of ToxAnalyzer by also using CTD data. For compounds having extensive information, manual data manipulation would be an overwhelming task. Our publication details the data manipulation performed by ToxAnalyzer, and how it deals with large volumes of data.
- 4 – Why ToxAnalyzer only shows the first 500 results of gene interactions? How are they are ordered?
- Only the first 500 interactions are shown to prevent slowing down the page or even crashing the user’s browser because of memory consumption. Gene interactions are ordered by organism alphabetical order.
- 5 – What if my desired dataset has more than 500 entries? How can I access the entire set of data?
- You can access the whole dataset by clicking on “Download all results”. The full dataset will be available offline as a .tsv file. It can be opened in a spreadsheet program or in a programming language specialized in data manipulation, such as R.
Can I run ToxAnalyzer on my computer?
Yes! You can download the ToxAnalyzer scripts here. Requires Python version 3.8 or higher, and the libraries urllib.request, pyplot, and pandas.
How to cite us?
We recently published a journal article on Computational Toxicology. If you use ToxAnalyzer on your research, please cite us. This helps to keep us improving the webtool:
Rodrigues, D. R., Mariano, D. C. B., Santos, L. H. S. & Tagliati, C. A. ToxAnalyzer: A user-friendly web tool for interactive data analysis and visualization of chemical compounds from the Comparative Toxicogenomics Database (CTD)™. Comput. Toxicol. 19, 100170 (2021). doi: 10.1016/j.comtox.2021.100170
We use data from the Comparative Toxicogenomics Database (CTD). Their last published peer-reviewed paper is:
Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., Wiegers, T. C. & Mattingly, C. J. Comparative Toxicogenomics Database (CTD): update 2021. Nucleic Acids Res. 49, D1138–D1143 (2021). doi: 10.1093/nar/gkaa891
Visit their website: http://ctdbase.org/
One of our group's papers has had its data inserted into CTD's database. Check it out!
Campos, M. A. A., de Almeida, L. A., Grossi, M. F. & Tagliati, C. A. In vitro evaluation of biomarkers of nephrotoxicity through gene expression using gentamicin. J. Biochem. Mol. Toxicol. 32, e22189 (2018). doi: 10.1002/jbt.22189