Figure 7.

Confidence Intervals (95% CIs) of the median bait-prey semantic similarity for SAINT-only and SAINT in conjunction with ROCS at the different ROCS procedural stages “N” (SAINT-only), “R”, and “S” (ROCS-SAINT) in the CTNNBIP1 (top) and STK24 (bottom) AP-MS bait experiments. Note especially the increase in median bait-prey semantic similarity between the naïve stage “N” (SAINT-only) and final stage “S” (ROCS-SAINT). The pairwise Resnik semantic similarity measure $sim\left(c_{\text{B}},c_{\text{P}}\right)$ is given between a Gene Ontology (GO) term from the bait protein (denoted c_B) and for each Specific Prey Protein (denoted c_P) as described in the methods section for all Gene Ontologies (Biological Process (BP), Molecular Function (MF), and Cellular Component (CC)) - see also Additional file 6: Table S4. Results are reported here for a conservative coefficient of $c=1.960$ for the 95% CI of the median since group sample sizes and group standard deviations were not similar (see Methods section), and for $C_S>{\widehat{C}}_S^{\mathit{cutoff}}$ and the marginal inclusion probability thresholds ${\tilde{p}}_{\text{min}}^C$ and ${\tilde{p}}_{\text{min}}^B$ as determined in each AP-MS experiment (see Tables 2 and 3).