Recovery of biological co-annotations from protein interactions. The proposed interaction detection based on shuffling (IDBOS) ranking scheme was compared with the frequency of occurrence ranking, one randomly ranked set (where the observed protein-protein interactions (PPIs) take random ranks), and a randomly rewired interaction set in retrieving biological relationships from diverse reference sets. The reference sets were: (A) co-pathway gene pairs, (B) co-disease susceptibility gene pairs, (C) functionally related gene pairs, and (D) tissue co-expressed gene pairs. We assessed performance by calculating the enrichment fraction of true PPIs among the judgeable interactions as a function of varying ranking thresholds. In the set scored by occurrence alone, multiple PPIs possessed the same score, and the second right-most symbol corresponds to the collection of PPIs with an observed occurrence ≥2.
Yu et al. BMC Bioinformatics 2012 13:79 doi:10.1186/1471-2105-13-79