Examples

A sample inputSmall.xlsx file has been provided and run through the pipeline. Simulations were run at 24 °C and with rna as material. Five human (-hsa) microRNAs, and one non-human (in this case c. elegans, -cel) microRNA, were chosen;

  • hsa-miR-21-5p

  • hsa-miR-23a-5p

  • hsa-miR-29a-5p

  • hsa-miR-141-5p

  • hsa-miR-148a-5p

  • cel-miR-39-3p


For each microRNA after running the first preprocessing_input step a radar plot is generated, the results of which are shown below:

TM-SmiRs radar plots


An iteractive plotly map was also generated as part of interactive_plotter. Background microRNAs were obtained from miRBase and consist of 2,656 mature microRNAs. These were used to construct the PCA embeddings; experiments were run at 24 °C and with rna as material. A CompositeScore was subsequently computed for each microRNA and superimposed on the plot. CompositeScore was defined as the normalised sum of radar plot variables GC content (%), purine content (%), free number of hydrogen bonds in the overall structure, and free number of hydrogen bonds in a six nucleotide toehold region, defined from the 5’ end was used. CompositeScore is a measure of how well a microRNA matches the desired hybridisation properties, with a higher score indicative of lower secondary structure (greater linearity) and more accessible binding regions.

Users are encouraged to hover over plots (they are interactive!) to see where input microRNAs were present. An intuitive visual understanding can be gained of which miRs are better suited for TMSD applications.