WAP and DEG scores for data set GSE58095.

A: c min P(j) values (blue solid line) and PFP values (red solid line, 104 permutations) as a function of their rank j. Dashed lines correspond to values obtained with a randomly rewired protein network and dotted lines to a randomly rewired network preserving the number of triangles. B: Scatterplot of WAP PFP and DEG FDR values. Thresholding DEG FDR and WAP PFP at 5% yields four categories of genes based on their significance: DEG and not WAP (green), DEG and WAP (red), WAP and not DEG (blue) and neither DEG nor WAP (gray).