Confidence scores assigned to the C. jejuni protein interactions. (a) The distribution of confidence scores generated for the CampyYTH v3.1 protein interactions are shown in red. The distributions of scores for the training sets containing likely true positives (green) or true negatives (black) are also shown. (b) Protein interaction pairs with high confidence scores (HCS; confidence scores > 0.5) share the same functions significantly more frequently (p value < 3 × 10-57) than protein pairs comprising interactions with low confidence scores (LCS; confidence scores ≤ 0.5). Protein 'self' interactions were excluded from the analysis. (c) The average depth of shared GO biological process annotation was determined for the interactions comprising each confidence score bin. Higher confidence interactions generally involve proteins with the same functional annotation at greater depths of precision. The two dotted line segments are linearly fitted lines between average GO depth and bin number in two regions, from 0.5 to 0.9 and 0.9 to 1.0. Protein 'self' interactions were excluded from the analysis.