Optimization of the weighting of the two networks in PIN. A) PIN was constructed by the optimized combination of two networks: A (enriched in membrane interactions) and B (the rest of BIOGRID). The Area Under Curve (AUC) of Precision-Recall plots for the top 5,000 interactions was used for selecting the optimum weight for network B using membrane proteins from GO Slim as an established benchmark dataset. The AUC was calculated for different weights for network B, and the weight corresponding to highest prediction performance and higher number of membrane interactions (AUC = 0.62) was chosen (weight of network B = 0.5). The increased coverage of membrane interactions reflected as the weight of network A (B) in the logistic regression is increased (decreased).
Brito and Andrews BMC Systems Biology 2011 5:169 doi:10.1186/1752-0509-5-169