Summary of the comparisons between PHENSIM and BioNSi.

We computed for both software accuracy, Positive Predictive Value (PPV), Sensitivity and Specificity for genes showing altered expression, and PPV and False Negative Rate (FNR) for the non-altered ones. The sample sets were categorized based on the KEGG meta-pathway genes: DS1 contains all sample sets where the up- or down-regulated gene was in KEGG; DS2 all the remaining ones. (XLSX)