Coverage of the interactome by BPMs.

G is the exact same set of interactions that was known to Kelley and Ideker in 2005; G′ is the more recent BioGRID network; G* is the slightly older network used by Ulitsky and Shamir. Ulitsky and Shamir's results A and B come from their supplementary Table S1, where A was generated using their “dense pathways” method and B using their “connected pathways” method. Ulitsky and Shamir treat synthetic-lethality and synthetic-sick interactions as equivalent; they cover 3,765 interactions in the combined set. Each BPM contributes two pathways to the enrichment calculations; we consider a pathway GO-enriched if the GO term has a depth of at least three in the hierarchy and p≤0.01 using FuncAssociate with an FDR multiple-testing correction. Both Kelley and Ideker as well as Ulitsky and Shamir use p≤0.05 with a hypergeometric test.