Fig. 3

Interactions filtering threshold. a F-Score against Reactome. 100-Fold validation. Averaged F-Score decreases after a cutoff of 0.4 suggesting that any threshold greater than 0.4 would lose Reactome’s interactions. b Network Expansion. Induced graph expansion on a starting set of about 400 vertices. By taking neighbors at distance two or three from seed nodes we captured almost the entire human interactome suggesting that the best choice was taking only the first neighbors. c Recall. Average fraction of seed proteins captured in both networks at each threshold. d Similarity between networks and random networks. Dashed lines show distance from random networks, continuous lines show distance between AD and PD networks. Distance 0, identical networks; distance 1, completely different networks. Difference between analyzed networks was of about 20 % at threshold 0.4, which was lower than the difference between these networks and random networks (40 %) suggesting the two networks at study are similar