Figure 1

Communities identified in the A and P Networks. Communities identified in the yeast protein interaction network for interactions of a) type A and b) type P. When the resolution parameter λ is very small, all nodes are assigned to the same community (which is analogous to viewing the network at a great distance). As λ is increased (viewing the network at progressively closer distances), more structure is revealed. The figures on the right hand side show visualisations of the networks' partition into communities at three different values of λ. Each circle represents a community, with size proportional to the number of proteins in that community, positioned at the mean position of its constituent nodes. (These positions were determined via a standard force directed network layout algorithm [57].) The shade of the connecting lines is proportional to the number of links between two communities. The main figure shows the communities that we find as we vary the resolution. We identify communities as the same through changing resolution parameter, and hence colour them the same, according to a convention described in the Methods (only communities of size 50 or more are shown). Note that the ordering of proteins is not the same in the two figures.