Figure 2

Signal integration in the yeast TR network. (A) The network of input (brown) and intermediate (purple) TFs is shown. The size of a node is proportional to the number of genes it regulates, while the width of a line connecting two nodes is proportional to the number of target genes jointly regulated by the two TFs. Except for Pdr3, Zap1 (input TFs) and Mot2 (intermediate TF), TFs are strongly connected to each other (i.e., share many of their target genes), indicating that the functions of the TFs are widely integrated, and that most genes are jointly or combinatorially regulated by groups of regulators, rather than individual ones. (B) Functional cartography in the network of TFs. Each node represents one TF and each link represents a regulatory interaction. The area of a TF node is proportional to the number of genes it regulates, and colors refer to the GO Slim annotation distributions of its target genes (see Methods for details). Input nodes are encircled by thick black lines. Regulatory links from input to intermediate TFs are shown in black, while links among intermediate TFs are colored red. The single unidirectional cycle connecting Dig1, Tec1 and Ste12 is shown by thick red edges. The portion enclosed in the dashed box is enlarged in panel C. (C) The overlapping origons Ino4 and Stb1 integrate cellular functions (see text for detailed analysis). Enlarged versions of panels A-C are provided as Supplementary Figure S2A-C.