FIG. 1.

Reconstructed networks for yeast response to stress. We used cDREM to reconstruct combinatorial networks for yeast heat shock response and yeast response to amino acid starvation. Each path represents a set of genes that are found to be expressed and regulated in a similar manner. Bright green nodes represent splits where a regulatory event is predicted to occur. The splits are associated with a predicted set of transcription factors (TFs) indicating that these TFs are responsible for the changes in gene expression at that time point. For each split we display the top five significant combinatorial relationships identified. Note that, because the focus here is on combinatorial analysis, we omit the single activators identified (e.g., HSF1 is found on the first upregulated path in heat shock). See Supplementary Data for a list of all predictions.