Simplify(TM) is for quantitative pathway analysis what MASCOT is for identifying proteins: data in and pathways out. Like MASCOT, it uses unbiased statistics which make very few assumptions about your data. You the user then decide where to “draw the line” and what to examine further.
By example, your favorite pathway might be present at low abundance; its regulation might consequently be difficult to detect. Considering all the pathway components, Simplify(TM) will give you the chance that this pathway is changing within the context of biological variability: p = 0.04, 0.12, 0.32? You then decide if you want to pursue further research.