The MIP repertoire is connected functionally to the transcriptome. (A) Graph showing the major functional categories that are overrepresented in the MIP repertoire of B-LCLs. Overrepresented functional categories were identified with the Ingenuity Pathway Analysis resource and are sorted by their statistical significance as follows: −log (P value calculated with the right-tailed Fisher exact test). Higher values indicate an increased association between the MIP source proteins and a given category. The dotted line represents the threshold for statistical significance (P < .05). Immune-associated categories are highlighted in red. More details on functional annotations represented in immune-associated categories are provided in supplemental Table 2. (B) The immunopeptidome of B-LCLs is connected functionally to the transcriptome of B-LCLs. An all-pairs-shortest-path matrix was used to calculate the functional association between MIP source proteins and the protein-coding transcriptome of B-LCLs (see “Functional connectivity score” for details). The functional association was measured as a connectivity score corresponding to the mean of the shortest path distance between every pair of proteins in an interaction network (ie, 1 MIP-source protein and 1 expressed transcript of B-LCLs). The red line represents the connectivity score between MIP source proteins and transcripts expressed by B-LCLs. A bootstrap procedure, represented by the Gaussian distribution, was used to calculate the control connectivity scores between MIP source proteins and random sets of the human transcripts. (*P < .0001).