Figure 2

Retrieving protein-protein interactions. The proposed interaction detection based on shuffling (IDBOS) ranking scheme was compared with hypergeometric test ranking, frequency of occurrence ranking, one randomly ranked set (where the observed protein-protein interactions [PPIs] take random ranks), a randomly rewired interaction set, and nine individual data sets. We compared these ranking schemes using benchmark reference sets derived from six independent experimental data sets, namely: (A) far-Western blotting, (B) isothermal titration calorimetry, (C) nuclear magnetic resonance, (D) surface plasmon resonance, (E) protein pairs in direct contact with each other within protein complex structures collected from PDB (contacts determined using the jointly buried surface area), and (F) mouse homologous protein interactions. We assumed that each reference set could only judge a PPI when each of its two proteins actually appeared in this reference set (judgeable). We assessed performance by coverage (number of true interactions) and accuracy (fraction of true interactions among judgeable interactions) as a function of varying ranking thresholds (when applicable). The higher-ranked thresholds are to the left in the plots. In the set scored by occurrence alone, multiple PPIs possessed the same score, and the second right-most symbol entry corresponds to the collection of PPIs with an observed occurrence ≥2.