Figure 3.

Usefulness of protein interaction networks. (a) The performance of five cases, including (i) random guess of localization, (ii) S features only, (iii) N¹ only, (iv) L¹ only and (v) all three kinds of features. (b–e) The performance of the N^D features for amino acid frequencies (b), chemical amino acid properties (c), and GO terms (d) as well as performance of the feature L^D (e). Performance is based on the five interaction networks BiG, DIP, SGD, Combined, and Random (different color curves). The performance of other N^D network features is shown in Supplementary Figure S3. The x-axis is the radius of neighborhood D; D = 0 means only the single protein feature vector S was used, which is a conventional approach. For Combined, the three interactome datasets BiG, DIP and SGD were pooled into a single network. For Random, localizations were randomly assigned on the BiG network. The solid lines and the dotted lines represent the Total and Balanced measures, respectively.