(A) Ratio of TPR to FPR for the MST, extended MST (eMST, α = 1) and connected (CON) approach on the complete Y2H network (Y2H all), the small-scale Y2H interactions (Y2H sc), the predicted interactions from Y2H experiments for other species (Y2H pred), the domain–domain interactions from the 3DID and iPfam databases (DD) and the core [Ito(C)] and non-core [Ito(NC)] interactions from the study by Ito et al. (2001). (B) TPR and FPR for decreasing values of α and the connected networks on the complete Y2H network. (C) Comparison of prediction accuracy of the MST, eMST and connected approach to the predictions by Bernard et al. (2007) (BVH) on the complete Y2H network. For this purpose, Y2H interactions from the studies of Uetz et al. (2000) and Ito et al. (2001) were not included in the calculation of TPR and FPR as they were used for training by Bernard et al. (2007).