Discrete gene sets were analysed using the Gene Set Enrichment Analysis with a slight modification to the scoring procedure to be more analogous to our continuous scoring procedure (described above). Specifically, we computed the average of the expression changes (defined by the t-statistic) for all genes within the discrete gene set upon knockdown63. Significance was assessed by permuting the control and sample labels and recomputing the average statistic for each permutation. The FDR was assessed off of these values as described above.
