  Background: If biology is modular then clusters, or communities, of proteins
derived using only protein interaction network structure should define protein
modules with similar biological roles. We investigate the link between
biological modules and network communities in yeast and its relationship to the
scale at which we probe the network.
  Results: Our results demonstrate that the functional homogeneity of
communities depends on the scale selected, and that almost all proteins lie in
a functionally homogeneous community at some scale. We judge functional
homogeneity using a novel test and three independent characterizations of
protein function, and find a high degree of overlap between these measures. We
show that a high mean clustering coefficient of a community 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.
