Dividing protein interaction networks for modular network comparative analysis

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