Figure 2

Schematic of the validation pipeline: 1) Expression data from a large number of experiments with control vs. perturbation samples; 2) The various approaches to differential expression are used to rank genes in order of significance; 3) Prior knowledge gene lists, for example genes associated with ChIP-Seq binding sites of the perturbed TF, are identified in the ranked list and the cumulative distribution is calculated; 4) The perturbation of the cumulative distribution from uniform is examined. Large deviations from zero, on the scale of φ, indicate significant prioritization of the prior knowledge genes. Also, the AUC distributions are examined across the various methods.