The self/nonself overlap of immunogenic versus non-immunogenic pMHCs.

For immunogenic or non-immunogenic HIV-1 peptides presented on HLA-A*0201 determined by Frankild et al. [9], for immunogenic and non-immunogenic vaccinia-derived peptides determined by Assarsson et al. [10], for immunogenic and non-immunogenic HIV-1 peptides on non-HLA-A*0201 determined by Perez et al. [37] and for immunogenic and non-immunogenic pMHCs sampled from the IEDB on HLA-A*0201 (see Methods for selection criteria applied to all four data sets), the presence of a self/nonself overlap was determined with the degenerate T-cell recognition model. For all sets of peptides, the immunogenic peptides have less overlaps with self, the significance of this association was tested using a Chi-square test, the p-value is reported in the last column.