Before revision:  We show that  high mean clustering coefficient and low mean node betweenness centrality can be used to predict functionally homogeneouscommunities. Availability: All the data sets and the community detection algorithm are available online .
After revision:  We show that high mean clustering coefficient and low mean node betweenness centrality can be used to identify those that are functionally homogeneous. By tracing the community membership of a protein through multiple scales we demonstrate how our approach could be useful to biologists focusing on a particular protein. Conclusions: We show that there is no one scale of interest in the community structure of the yeast protein interaction network, but we can identify the range of resolution parameters that yield the most functionally coherent communities, and predict which communities are most likely to be functionally homogeneous .