Estimating the Reliability of Protein-Protein Interactions

Many methods developed for estimating the reliability of protein-protein interactions are based on the topology analysis of protein-protein interaction networks. This paper describes a new reliability measure of protein-protein interactions, which is theoretically rigorous, yet biologically meaningful. The new measure does not rely on the topology of protein interaction networks, but formulates the biological information on functional roles, sub-cellular localizations and protein classes into a theoretically rigorous scoring scheme. Comparison of the new measure with IG1, IG2, and IRAP shows that the new measure is better than IG1 and IG2, and slightly better than IRAP. The new measure will be useful for filtering many spurious interactions as well as for estimating the reliability of protein interaction data.