Figure 5

Extending the currently known parts of the regulatory network and breaking it down into state dependent networks [see Additional files 2]. Here we display a representative subset of known and predicted links in the yeast regulatory network along with categories of experimental conditions in which the target genes are controlled by their regulators. To simplify the display, we aggregated the experimental conditions into categories such as cell cycle (green links), amino acid starvation (orange), rapamycin treatment (blue), and alpha-factor treatment (purple). TFs are represented by squares and their target genes by circles. Solid and dotted links indicate the known and predicted regulatory links, respectively. The predicted experimental conditions in a UTM corresponding to a regulatory link tend to contain the experimental condition in which a TF binding on the promoter region of a target gene has been experimentally confirmed[6]. For example, the predicted regulatory links STE12→FUS2 and TEC1→GFA1 are supported by ChIP-on-chip location analyses performed with alpha factor pheromone treatment (purple-dotted links STE12→FUS2 and TEC1→GFA1).