Figure 2

Functional co-occurrence rates of interacting protein pairs sorted by their similarity in a descending order. We compared three similarity measurements by functional co-occurrence. The interaction data from DIP were used. For each interacting protein pair, we measured the structure-based similarity in Formula 13, the annotation-based similarity in Formula 14 and connectivity-based interaction reliability in [33]. For the structure-based and annotation-based similarity, we used the GO terms and annotations in Biological Process and Molecular Function categories. We then sorted the pairs by their similarity in a descending order, and calculated the average functional co-occurrence rates for every 500 pairs. That is, we inspected how many pairs among 500 pairs co-occurred in the same functional categories from FunCat in MIPS. The interacting pairs with high structure-based and annotation-based similarity have higher rates of functional co-occurrence than those with high connectivity-based reliability. Moreover, in the range of top 4000 pairs, the annotation-based similarity performs better than the structure-based similarity.