Figure 1

Global organization of the yeast transcriptional-regulatory network. (A) The hierarchical arrangement of the TR network into input, intermediate and output layers (rectangles, ellipses, and small circles, separated by dashed lines, respectively) is illustrated for two partially overlapping origons, Yap1 and Skn7. The boxes illustrate 3-node subgraphs, CNV, CMR, and FFL distinguished by their high frequency of occurrence in the yeast TR network (Table 1). (B) The network of origons [13] in the S. cerevisiae TR network. Each circle represents an origon labeled by its input TF. The size of each circle is proportional to the number of genes in that origon. Two origons are connected if they share at least one gene and the width of a link is proportional to the number of genes that the two connected origons share. Three different types of subgraphs, indicated by the colored labels are distinguished in the origons (see Table 1). The fractional area of each color on the origon circle is proportional to the number of occurrences of the corresponding subgraph among the members of the origon. If an origon contains none of the listed subgraphs, it is shown in grey color. (C) Main panel: the distribution of outdegrees (number of outgoing connections of a node, k _out ) shows that this network falls between models with an exponential or faster degree distribution cutoff [14,17] and the scale-free model [15] (with some difference for input and intermediate TF nodes), though neither of the two types of models is significantly closer than the other.