Before revision:  We thus not only identify complexes from the interaction data but also larger collections of strongly-interacting proteins . Communities that contain interactions from tandem affinity purification and co-immunoprecipitation data are far more likely to be biologically homogeneous than those from yeast-two-hybrid and split-ubiquitin data. We find that high clustering coefficient is a very good indicator of biological homogeneity in small communities. For larger communities, we find that link density is also important. Our results significantly improve the understanding of the modular structure of the protein interaction network- and how that modularity is reflected in biological homogeneity and experimental type. Our results suggest a method to select groups of functionally similar proteins even when no annotation is yet known, thereby yielding a valuable diagnostic tool to predict groups that act concertedly within the cell .
After revision:  We thus not only identify complexes from the interaction data but also larger collections of strongly-interacting proteins . Communities that contain interactions from tandem affinity purification and co-immunoprecipitation data are far more likely to be biologically homogeneous than those from yeast-two-hybrid and biological function to select groups of functionally similar proteins even when no annotation is yet known, thereby yielding a valuable diagnostic tool to predict groups that act concertedly within the cell .