Figure 3

Overlap of top-ranked protein interactions. The overlap of top-ranked protein-protein interactions (PPIs), based on a pairwise comparison of three interaction evaluation schemes: interaction detection based on shuffling (IDBOS), hypergeometric test ranking, and frequency of occurrence ranking. The overlap between hypergeometric and occurrence rankings was considerable. The right-most point in the graph corresponds to the case where all interactions are included and, by definition, the three schemes overlap. For intermediate rankings, IDBOS shows considerably lower overlap with either method, indicative of distinct and different sets of top-ranked PPIs. The right-most curve (Random) shows the expected overlap fraction of top-ranking PPIs from two completely random rankings, emphasizing that even though the overlap fraction between IDBOS and Occurrence ranking was low, it was considerably higher than what would be expected by chance alone.