Figure 3. Evaluation of AP-MS Protein Interactions.
(A) AP-MS interactions superimposed onto CORUM complexes. The pie chart depicts the fraction of complexes achieving the indicated coverage in BioPlex. Only complexes containing two or more baits were considered. Five representative CORUM complexes: baits are colored blue, while preys are red and proteins not observed by AP-MS are gray. Interactions among CORUM complex members are gray while interactions confirmed by AP-MS are red.
(B) Physical protein interactions reported in BioGrid, CORUM, GeneMania, STRING, and MINT were merged. Left: overlap among databases. Right: overlap among databases for interactions confirmed by AP-MS.
(C) Fraction of database interactions confirmed by AP-MS as a function of the number of supporting database reports. The composite interaction database was filtered to include only interactions connecting one of 2594 baits with proteins observed as baits or preys in the interaction network.
(D) 86% of AP-MS interactions have not been reported in the databases listed above.
(E) Pairwise comparisons of BioPlex with published interaction networks were performed, using graph assortativity to quantify preferential interaction in cases of shared localization among proteins detected in both networks. Literature datasets included BioGRID, CORUM, GeneMania, STRING, and MINT, as well as interactions recently reported via yeast-two-hybrid (Rolland et al., 2014) and LC-MS correlation profiling (Havugimana et al., 2012). Each analysis was repeated with randomized localizations as a control.