Figure 6.

The overlap significance obtained from the most likely models vs. that obtained from simple direct model on Chua et al.’s data. note: different symbols denote the type of models for which the most overlap significance occurs. I: simple direct model; II: PTM-mediated direct model; III: two-layer cascade regulation model; IV: PTM-mediated two-layer cascade regulation model; V: hybrid two-layer cascade regulation model; VI:three-layer cascade regulation model. TFs with red fonts denote those correctly identified in overexpression experiments. TFs with green fonts denote those correctly identified in deletion experiments. TFs with large size of fonts denote those correctly identified in the most likely model but missed in Model I. The number in the red rectangle denotes the rank of the TF in the list of candidates (the rank obtained by our method/ the rank obtained if only Model I was used).