BioPAN has been developed to perform a pathway analysis from lipidomics dataset. This dataset must be in the CSV format (Comma-Separated Values) and contain quantitative data.
After loading the file, LipidLynxX 1 is launched to convert the lipid molecular species naming to the BioPAN nomenlature. Then, a summary of the lipid molecular species in the input file is available (unrecognised/processed/unprocessed species). It is then asked to assign a condition to each sample.
Finally, it is possible to choose the type of analysis to be performed using the menus on the left:
Pathway options: which type of analysis do you want to perform? Which status do you want to display? At which lipid level? And against which subset of lipid data? Which conditions do you want to compare?
Pathway calculation: which detection threshold do you want to use? Do you have paired data?
With the selected options, BioPAN will search for pathways and calculate a score per reaction. This score will indicate the shift toward more (or less) product or reactant in interest samples than control samples. It will be used to predict whether a particular reaction is active (or suppressed) or not using statistics. The pathways are available on the graph(s) displayed in the viewport and the legend on the left part of the page. The results are stored at the bottom of the page through 4 tables (all/lipid class/lipid species/fatty acids results). You will be able to access your current analysis for 30 days.
Let’s try bioPAN using a demonstration file to understand how BioPAN works! And if you want to have more details, look at the documentation.