Fig. 6

Illustration of the construction of contrast scores. a 1vs1 enrichment analysis. b 2vs1 differential analysis (left) or enrichment analysis (right). In each panel, an interesting feature (top) and an uninteresting feature (bottom) are plotted for contrast; both features have measurements under the experimental and background conditions. In a, each feature’s measurements are summarized into a maximum (max) contrast score or a minus contrast score. In b, each feature’s measurements are permuted across the two conditions, resulting in two sets of permuted measurements. Then for each feature, we calculate its degrees of interestingness—as the difference that equals the average of experimental measurements minus the average of background measurements (in enrichment analysis; right), or the absolute value of the difference (in differential analysis; left)—from its original measurements and permuted measurements, respectively. Finally, we summarize each feature’s degrees of interestingness into a maximum (max) contrast score or a minus contrast score