Integrating network topology, gene expression data and GO annotation information for protein complex prediction

The prediction of protein complexes based on the protein interaction network is a fundamental task for the understanding of cellular life as well as the mechanisms underlying complex disease. A great number of methods have been developed to predict protein complexes based on protein–protein interaction (PPI) networks in recent years. However, because the high throughput data obtained from experimental biotechnology are incomplete, and usually contain a large number of spurious interactions, most of the network-based protein complex identification methods are sensitive to the reliability of the PPI network. In this paper, we propose a new method, Identification of Protein Complex based on Refined Protein Interaction Network (IPC-RPIN), which integrates the topology, gene expression profiles and GO functional annotation information to predict protein complexes from the reconstructed networks. To demonstrate the performance of the IPC-RPIN method, we evaluated the IPC-RPIN on three PPI networks of Saccharomycescerevisiae and compared it with four state-of-the-art methods. The simulation results show that the IPC-RPIN achieved a better result than the other methods on most of the measurements and is able to discover small protein complexes which have traditionally been neglected.