Figure 2

Degree of common annotation in interacting protein pairs in experimental and inferred networks. A) Schematic representation of the algorithm used to evaluate the relatedness of gene ontology annotation. The Gene Ontology graph induced by protein 'i ' is in green, while the one induced by protein 'j' is in blue. Dij is the number of edges that the two induced graphs have in common. B) For any given network we have derived a 'scrambled network' containing the same protein nodes linked by the same number of edges with their connections rearranged at random. For each interacting protein pair, in which both proteins have a GO annotation, we have then calculated Dij. Finally we have plotted, as a function of Dij, the difference between the percentage of nodes having a specific Dij in the inferred and in the scrambled network.