Figure 4

FDR and GO semantic similarity analyses in the CTNNBIP1 AP-MS bait experiment. Left: Log-plot of FDR estimates for the bait-prey PPIs are plotted against Confidence Score cutoffs [see also Additional file 2: Figure S7. Right: plot of distance d estimates of bait-prey GO semantic similarity measures (see Methods section) are plotted against Confidence Score cutoffs [see also Additional file 2: Figure S7. Estimates of log ₁₀(10⁻³ + FDR) and d are reported with standard errors in both cases. Horizontal black dotted lines correspond to thresholds of significance levels for FDR (θ = 0.05) and GO (d > 0). For the computation of d, approximate 95% Confidence Interval of median bait-prey semantic similarities were carried out in the initial set of bait experiments (“N” stage) and the set of bait Reproducible Experimental Replicates (“S” stage) for the Molecular Function (MF) ontology as described in method section. Here B = 1024 Monte-Carlo replicates were performed, and a coefficient c = 1.386 was chosen for the 95% CI since group sample sizes and group standard deviations were similar [32]. Results are reported for the positive range of Confidence Score cutoff Ĉ _S ^cutoff ∈ (0, 0.2] and for the marginal inclusion probability threshold ${\tilde{p}}_{\text{min}}^B=0.75$.