Construction of reliable protein–protein interaction networkswith a new interaction generality measure

Motivation: Recent screening techniques have made large amounts of protein–protein interaction data available, from which biologically important information such as the function of uncharacterized proteins, the existence of novel protein complexes, and novel signal-transduction pathways can be discovered. However, experimental data on protein interactions contain many false positives, making these discoveries difficult. Therefore computational methods of assessing the reliability of each candidate protein–protein interaction are urgently needed. Results: We developed a new ‘interaction generality’ measure (IG2) to assess the reliability of protein–protein interactions using only the topological properties of their interaction-network structure. Using yeast protein–protein interaction data, we showed that reliable protein–protein interactions had significantly lower IG2 values than less-reliable interactions, suggesting that IG2 values can be used to evaluate and filter interaction data to enable the construction of reliable protein–protein interaction networks. Availability: The protein–protein interaction data used in this study along with the associated IG2 values are available at http://genome.gsc.riken.go.jp. Contact: rgscerg@gsc.riken.go.jp * To whom correspondence should be addressed. † Present address: Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.