Fully automated data analysis:
For data analysis, we have developed a dedicated software tool, ToxPlot. Toxplot enables automated data analysis and graphical representation of the test results allow clear and rapid assessment of the reactive properties of novel compounds. ToxPlot visualises induction of the ToxTracker reporters in a easy interpretable heatmap.
- ToxPlot©, custom-made software (windows, macOS, linux)
- Automated data integration for GFP reporter activation and toxicity
- Statistical analysis, data clustering and heatmap creation
Toxplot is a collection of custom scripts written in the R statistical analysis language. Toxplot imports the raw data files in CSV format that are generated by the flow cytometer (this has been tested for different types of cytometers) and that contain for each exposure data on the MFI and cell concentration. Following calculation of GFP induction as well as cytotoxicity levels, GFP fold induction is plotted against cytotoxicity. The extent of GFP induction at a particular level of cytotoxicity is calculated by linear regression between the two adjacent cytotoxicity measurements. Next, GFP induction levels for each of the ToxTracker reporters are used for hierarchical clustering of the analyzed compounds based on similarity of reporter activation. Results are visualized in a heat map. Toxplot is run on an independent server in our facilities. The software functions as stand alone software.
Comparison of results to database of reference compounds
Toxplot does not only calculate the results for the current assays, but can also compare results to a large database of compounds. Every compound tested in ToxTracker has a unique fingerprint reponse to the various reporter genes. These fingerprints are stored and added in the software. New results can then be compared by hierarchical clustering to the known compounds in the system. For customer compounds we only add a reference name, but the fingerprints are never shared.
ToxPlot output – heatmap
ToxPlot output of the preferential induction of the ToxTracker reporters. The hue of green indicates the relative induction of the different ToxTracker reporters at compound doses that resulted in 50% cell survival. Reporters with similar specificity and chemicals with comparable reactivity are clustered.