|Overlap and semantic similarity analyses between the ROCS’s lists of Specific Prey Proteins with those obtained by SAINT and ComPASS in all bait experiments (see also Additional file 5: Table S3)|
|Bait Experiment||ROCS Unique Prey Proteins (NB)||ROCS Unique Specific Prey Proteins (SB)||SAINT Unique Specific Prey Proteins (B)||SAINT Intersection (X)||SAINT Intersection Significance (p-value)||
SAINT Semantic Similarity
|Bait Experiment||ROCS Unique Prey Proteins (NB)||ROCS Unique Specific Prey Proteins (SB)||ComPASS Unique Specific Prey Proteins (B)||ComPASS Intersection (X)||ComPASS Intersection Significance (p-value)||
ComPASS Semantic Similarity
Using a similar overlap analysis by means of the hypergeometric distribution test and GO semantic similarity as in Table 4, we determined the statistical significance of the overlap between: (Top ) ROCS vs. SAINT, and (Bottom) ROCS vs. ComPASS for all gene ontologies (Biological Process (BP), Molecular Function (MF), and Cellular Component (CC)) and in all bait experiments. SAINT and ComPASS lists are reported for PSAINT > 0 and D − score > 0 respectively. ROCS lists are reported for C − score CS > ĈScutoffand the marginal inclusion probability thresholds and as determined in each AP-MS experiment.
Dazard et al.
Dazard et al. BMC Bioinformatics 2012 13:128 doi:10.1186/1471-2105-13-128