Figure 3

Cooperation types of correlated genes. Figure 3 shows the types of cooperative correlations between a module pair and its correlated genes predicted by our method. We predicted genes that mediate cooperative interactions between a pair of modules by evaluating the significance of the number of direct physical interactions between each module of a module pair and genes in the weighted interactions network (WPI network) with random networks (Figure 2). We used a yellow circle to indicate a gene and a green box to indicate a module. Consider a gene x in the WPI network and an identified module pair. If the number of protein-protein interactions (or regulatory interactions from ChIP-chip data) between x and a module is significant, the association was presented by a blue undirected line (or a red directed line) between the circle and a box. We identified five types of correlative associations: (A) A significant number of undirected links between x and genes in one of the modules and a significant number of directed links from genes in the other module to x in the WPI network. (B) A significant number of undirected links between x and genes in one of the modules and a significant number of directed links from x to genes in the other modules in the WPI network. (C) A significant number of undirected links between x and genes in each of the two modules in the WPI network. (D) A significant number of directed links from genes in each of the two modules to x in the WPI network. (E) A significant number of directed links from x to genes in each of the two modules in the WPI network.