Table 1.
Allele | # Peptides | ANN | ARB | SMM | MHC-PPM | ||
---|---|---|---|---|---|---|---|
9 | 10 | ||||||
9-mers + 10-mers | HLA-A*0201 | 3089 | 1316 | - | 0.919 | 0.939 | 0.931 |
HLA-A*0202 | 1447 | 1056 | - | 0.851 | 0.879 | 0.871 | |
HLA-A*0203 | 1443 | 1055 | - | 0.838 | 0.878 | 0.882 | |
HLA-A*0301 | 2094 | 1082 | - | 0.883 | 0.915 | 0.911 | |
HLA-A*0206 | 1437 | 1054 | - | 0.849 | 0.890 | 0.885 | |
HLA-A*1101 | 1985 | 1093 | - | 0.897 | 0.932 | 0.937 | |
HLA-A*2402 | 197 | 78 | - | 0.722 | 0.809 | 0.833 | |
HLA-A*3101 | 1869 | 1057 | - | 0.881 | 0.903 | 0.878 | |
HLA-A*3301 | 1140 | 1055 | - | 0.866 | 0.888 | 0.863 | |
HLA-A*6801 | 1141 | 1055 | - | 0.827 | 0.874 | 0.864 | |
HLA-B*0702 | 1262 | 205 | - | 0.925 | 0.952 | 0.954 | |
HLA-B*3501 | 736 | 177 | - | 0.833 | 0.886 | 0.866 | |
HLA-B*5101 | 244 | 177 | - | 0.782 | 0.875 | 0.886 | |
HLA-B*5301 | 254 | 177 | - | 0.758 | 0.854 | 0.847 | |
9-mers | HLA-A*0101 | 1157 | - | 0.982 | 0.964 | 0.980 | 0.963 |
HLA-A*2601 | 672 | - | 0.956 | 0.907 | 0.931 | 0.901 | |
HLA-A*2902 | 160 | - | 0.935 | 0.755 | 0.911 | 0.907 | |
HLA-A*6802 | 1434 | - | 0.899 | 0.865 | 0.898 | 0.867 | |
HLA-B*0801 | 708 | - | 0.955 | 0.936 | 0.943 | 0.926 | |
HLA-B*1501 | 978 | - | 0.941 | 0.900 | 0.952 | 0.922 | |
HLA-B*1801 | 118 | - | 0.838 | 0.573 | 0.853 | 0.906 | |
HLA-B*2705 | 969 | - | 0.938 | 0.915 | 0.940 | 0.938 | |
HLA-B*4002 | 118 | - | 0.754 | 0.541 | 0.842 | 0.891 | |
HLA-B*4402 | 119 | - | 0.778 | 0.533 | 0.740 | 0.891 | |
HLA-B*4403 | 119 | - | 0.763 | 0.461 | 0.770 | 0.847 | |
HLA-B*5401 | 255 | - | 0.903 | 0.847 | 0.921 | 0.883 | |
HLA-B*5701 | 59 | - | 0.826 | 0.428 | 0.871 | 0.929 | |
HLA-B*5801 | 988 | - | 0.961 | 0.889 | 0.964 | 0.944 | |
Average (All) | 0.888 | 0.798 | 0.893 | 0.897 | |||
Average (9mers) | 0.888 | 0.751 | 0.894 | 0.908 | |||
Weighted Avg | 0.932 | 0.872 | 0.910 | 0.901 |
The best-performing method for each allele is underlined. The given AUC values for ARB and SMM are the weighted averages of the AUC values for 9-mers and 10-mers based on the given peptide counts for a specific allele. The alleles in the bottom part of the table were only trained & tested in 9-mers and are directly comparable.