A Novel Network-Based Algorithm for Predicting Protein-Protein Interactions Using Gene Ontology

Proteins are one of most significant components in living organism, and their main role in cells is to undertake various physiological functions by interacting with each other. Thus, the prediction of protein-protein interactions (PPIs) is crucial for understanding the molecular basis of biological processes, such as chronic infections. Given the fact that laboratory-based experiments are normally time-consuming and labor-intensive, computational prediction algorithms have become popular at present. However, few of them could simultaneously consider both the structural information of PPI networks and the biological information of proteins for an improved accuracy. To do so, we assume that the prior information of functional modules is known in advance and then simulate the generative process of a PPI network associated with the biological information of proteins, i.e., Gene Ontology, by using an established Bayesian model. In order to indicate to what extent two proteins are likely to interact with each other, we propose a novel scoring function by combining the membership distributions of proteins with network paths. Experimental results show that our algorithm has a promising performance in terms of several independent metrics when compared with state-of-the-art prediction algorithms, and also reveal that the consideration of modularity in PPI networks provides us an alternative, yet much more flexible, way to accurately predict PPIs.