We assess COG category recovery for the four individual methods, the combination of the four methods, and TextLinks. (a) We assign a confidence measure to the likelihood that a pair of proteins is acting within the same COG pathway, reflecting the number of COG-annotated pairs that lie within the same pathway relative to the total number of annotated pairs. The COG confidence metric is used in the network-graphing function of the Proteome Navigator to select inferred protein linkages with uniform confidence. E. coli protein pairs displayed in this figure have a COG pathway confidence recovery (cumulative accuracy) of greater than 0.4, with the exception of the TextLinks pairs. (b) The receiver operator characteristic (ROC) curve shows the performance of the rank-ordered list of all E. coli interactions predicted from genomic inference (solid line) compared with the random selection of protein pairs (dashed line).