Figure 4

(a) Functional co-occurrence and (b) functional consistency of interacting protein pairs with respect to their functional similarity. We investigated the functional co-occurrence and functional consistency of the interacting protein pairs from DIP with respect to their functional similarity rates in the range between 0 and 1. The similarity was measured by Formula 13 and 14. As the similarity by both measurements becomes higher, the functional co-occurrence and consistency monotonically increase. However, the annotation-based similarity performs better than the structure-based similarity because there are not enough variations of functional co-occurrence and consistency up to 0.7 of the structure-based similarity. It indicates that the annotation-based method correctly quantified the functional similarity of interacting proteins.