Fig. 1.

PMNs physical module. (a) Expression pattern of the Mob1 regulator (top) and its 37 target genes (bottom), during 2 cell cycles (two replicates are shown). (b) A physical pathway connecting Mob1 via Cdc28 to the transcription factor FKH2 that binds 15 of the module genes. (c) Learning procedure. Input: gene expression, a set of potential regulators and physical protein–protein and protein–DNA interactions. PMN Learner: an iterative optimization procedure that finds modules, their regulators and the physical pathways that explain the regulation. Output: the best configuration found by the learner.