Inferring protein-protein interactions using interaction network topologies

We describe two novel methods for predicting protein interactions, using only the topology of an observed protein interaction network. The first method searches the protein interaction network for defective cliques (i.e. nearly complete complexes of pairwise interacting proteins), and predicts the interactions that complete them. The second method computes the diffusion distance between each pair of proteins and then infers an interaction when such distance is below a given threshold. We show that both methods have a good predictive performance and compare their results.