Fig. 3

Relaxed similarity between overall and threshold ranks in the scored PINs. a The overall ranks have been calculated over the medium-high confidence regions—0.60 to 0.90 for the three STRING networks (black dotted lines) and 0.15 to 0.28 for the HitPredict network (pink dotted lines). b The STRING medium-high confidence interval was also used for the synthetic networks. The SYN-GNP network, where both structure and score allocation are uniform, exhibits lower relaxed similarity. The SYN-PVX network has inherently heterogeneous network structure, on which scores are assigned randomly. Score thresholding introduces the same rate of change in different parts of the network, so that the relative node degree, for example, may remain largely unchanged across a series of thresholds. In contrast, the heterogeneous score allocation in PINs makes rank reorderings more likely, and identifiability may be expected to be lower