Protein Hypernetworks: a Logic Framework for Interaction Dependencies and Perturbation Effects in Protein Networks

Results: We present an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining protein hypernetworks. First we demonstrate how this framework straightforwardly improves the prediction of protein complexes. Next we show that modeling protein perturbations in hypernetworks, rather than in networks, allows to better infer the functional necessity of proteins for yeast. Furthermore, hypernetworks improve the prediction of synthetic lethal interactions in yeast, indicating their capability to capture high-order functional relations between proteins.