Figure 1

PPI prediction test results of semantic similarities in BP ontology with and without IEA annotations. Eight different methods were tested for PPI prediction by gradually decreasing the threshold of semantic similarity scores. The semantic similarities were measured in BP ontology (a) with IEA annotations and (b) without IEA annotations. In (a), simICND, simICNP and Jiang's method perform the best. In particular, simICND outperforms the others when the false-positive rate is less than 0.3.