Figure 3

Assessment of CAPPI-Pred predictions. Assessment of CAPPI-Pred predictions. (A) and (B): Histograms of BP scores for the predicted yeast (A) and human (B) PPI datasets of the same size (1576 yeast PPIs and 17105 human PPIs) from the Interlog method, CAPPI-Pred and CAPPI-Integ. (C) and (D): The ratio of true positives and false positives as a function of the number of interactions in yeast (C) and human (D). An interaction is deemed true positive if it is found in the reference dataset of either co-complex interactions (Complex) or binary PPIs (PPI), or in any available reference set (ALL) and false positive, if the proteins are assigned different cellular localization (see text). Plots labeled as "Filtered Complex" and "Filtered PPI" show the results of selected CAPPI predictions which are part of dense clusters tested against either the co-complex reference (Complex) or binary reference (PPI). The gray dashed line marks the level at which the number of true positive predictions is equal to the number of false positive predictions.