Figure 2

Enrichment of “known” (iPFAM) domain-domain interactions. Evaluation of the top-scoring domain-domain interactions (DDIs) extracted by the parameter-dependent DDI selection (PADDS) and the generalized parsimonious explanation (GPE). (A) The fraction of known DDIs in the iPFAM database [38] retrieved by PADDS as a function of α and the number of top-scoring DDIs. (B) Comparison of the percentage of retrieved iPFAM DDIs using PADDS and GPE as a function of top-ranked DDI sets (i.e., recall). (C) Comparison of the fraction of retrieved iPFAM DDIs using PADDS and GPE as a function of the iPFAM DDI set and top-ranked DDI sets (i.e., precision). For the GPE sets, we used the DDI rank information provided with the published data that includes their designated high-confidence (GPE-HC) and low-confidence (GPE-LC) sets [21]. We have also indicated the best results achievable with any α value, typically achieved for α = 0.1.