Effect of TRN properties. We used Networks 1, 2 and 2 of Fig. 2 to generate 100 synthetic expression data sets, and eliminated 50% of the gene/TF interactions in the TRN. Shown is the percentage of the deleted network recovered as a function of success rate. As the number interactions increases, the percentage of the network that can be recovered decreases. b) Same as a) except we used Network 1 and eliminated 25%, 50%, and 75% of the network. As expected, higher percentage of the deleted network is recoverable when a more complete network is known.