Fig. 4.

PPI quality metrics for benchmark datasets and high and low confidence D. vulgaris protein pair sets. The top three rows show metrics for benchmark bacterial datasets: the EcoCyc complexes (53) and protein pairs that have been reciprocally confirmed in either four AP-MS studies, including ours, or in six Y2H studies (supplemental Table S3). The remaining rows show metrics for our high confidence set and the four low confidence sets of protein pairs described in the text. The numbers of protein pairs in each set are given in parentheses. The columns shows from left to right are as follows: percent of pairs whose members are encoded in the same operon; reciprocal PPI confirmation percent; fold enrichment of pairs for which both members have the same TIGR role over that expected among randomly chosen pairs; percent overlap with a combined set of interologs from the six bacterial Y2H interactomes; and percent overlap with a combined set of interologs from the three published bacterial AP-MS interactomes (see “Experimental Procedures” for more details).