Figure 2

For a) the A network b) the P network, i) the number of communities of size four or more and ii) the number of proteins in such communities and the fraction of these that are judged functionally homogeneous. i) The number of communities with changing resolution parameter (solid black curve) ii) The number of proteins p in communities of size four or more (solid black curve). Also shown are the numbers of communities/proteins in such communities judged to be functionally homogeneous according to the GO similarity measure (green curves), the MIPS measure (dot-dashed blue curves) and the correlated growth similarity measure (dashed red curves). At values of log(λ) ≤ 0.5, relatively few proteins are in communities judged to be functionally homogeneous. The curves are similar for both networks, and they show a similar proportion of proteins in functionally homogeneous communities. One difference is that there are more proteins in functionally homogeneous communities at a lower value of log(λ) for the P network.