Method overview. (A) Transcriptional modules were inferred by searching for motif combinations that were overrepresented in a set of co-expressed genes. Co-expression was defined by a correlation threshold to a central gene, and an exhaustive search was conducted with all genes as centers and applying all thresholds. (B) The regulatory control of each module was inferred by iteratively trying more complex combinations of transcription factors, and stopping when no significant improvement in correlation between observed and predicted expression could be observed. (C) A network was constructed based on the modules and their best transcription factor combinations. (D) The network was validated statistically by bootstrap analysis to test the stability and predictive capabilities.