Motivating examples of the value of PED. (A) The TF Oct4 shows strong correlation with its functional target gene Dppa5a, even though expression is measured from a diverse collection of tissues, diseases, and cell types by different labs. In contrast, a random gene only shows weak to zero correlation with the TF (bottom-right corner). (B) The transcriptional repressor Jarid2 shows strong negative correlation with its functional target gene Slc48a1. Again, the correlation between the TF and a random gene is weak (bottom-right corner). The plots are based on 9,634 samples in a compendium of GPL1261 Affymetrix Mouse 430 2.0 arrays, where each dot corresponds to measurements from a single microarray sample.