Dividing Protein Interaction Networks for Modular Network

6 The increasing growth of data on protein-protein interaction (PPI) networks has boosted research 7 on their comparative analysis. In particular, recent studies proposed models and algorithms for 8 performing network alignment, that is, the comparison of networks across species for discovering 9 conserved functional complexes. In this paper, we present an algorithm for dividing PPI networks, 10 prior to their alignment, into small sub-graphs that are likely to cover conserved complexes. This 11 allows one to perform network alignment in a modular fashion, by acting on pairs of resulting small 12 sub-graphs from different species. The proposed dividing algorithm combines a graph theoretical 13 property (articulation) with a biological one (orthology). Extensive experiments on various PPI 14 networks are conducted in order to assess how well the sub-graphs generated by this dividing 15 algorithm cover protein functional complexes and whether the proposed pre-processing step can 16 be used for enhancing the performance of network alignment algorithms. Source code of the 17 dividing algorithm is available upon request for academic use. 18