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Table 1 Predictive performance of immunoproteasome and proteasome cleavage models

From: Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome

Immunoproteasome
Size SE SP ECS MCC BTR
4 0.807 ± 0.030 0.851 ± 0.039 47.828 ± 2.001 0.660 ± 0.038 0.329 ± 0.016
6 0.763 ± 0.036 0.708 ± 0.042 38.495 ± 0.614 0.472 ± 0.069 0.378 ± 0.016
8 0.906 ± 0.023 0.545 ± 0.038 51.219 ± 1.008 0.484 ± 0.059 0.394 ± 0.011
10 0.802 ± 0.024 0.462 ± 0.019 39.083 ± 1.003 0.281 ± 0.045 0.411 ± 0.012
12 0.903 ± 0.031 0.407 ± 0.031 46.339 ± 0.481 0.357 ± 0.062 0.439 ± 0.014
14 0.872 ± 0.035 0.374 ± 0.023 43.190 ± 1.498 0.284 ± 0.056 0.434 ± 0.017
16 0.855 ± 0.030 0.306 ± 0.041 41.908 ± 1.406 0.193 ± 0.047 0.436 ± 0.015
18 0.857 ± 0.031 0.290 ± 0.028 42.536 ± 1.081 0.179 ± 0.039 0.432 ± 0.015
Proteasome
Size SE SP ECS MCC BTR
4 0.803 ± 0.125 0.871 ± 0.052 44.110 ± 9.249 0.681 ± 0.089 0.362 ± 0.069
6 0.792 ± 0.048 0.723 ± 0.037 36.274 ± 1.943 0.516 ± 0.082 0.429 ± 0.023
8 0.855 ± 0.037 0.603 ± 0.047 38.160 ± 2.112 0.473 ± 0.072 0.473 ± 0.019
10 0.885 ± 0.050 0.537 ± 0.046 37.839 ± 2.355 0.452 ± 0.069 0.506 ± 0.025
12 0.874 ± 0.034 0.534 ± 0.062 34.970 ± 1.704 0.434 ± 0.075 0.526 ± 0.017
14 0.871 ± 0.037 0.468 ± 0.065 33.699 ± 1.432 0.371 ± 0.085 0.532 ± 0.018
16 0.844 ± 0.058 0.403 ± 0.065 32.657 ± 1.692 0.276 ± 0.096 0.518 ± 0.027
18 0.794 ± 0.077 0.392 ± 0.060 27.510 ± 1.978 0.206 ± 0.126 0.519 ± 0.035
  1. Cleavage models were built on peptide fragments of a given size encompassing the C-terminal end of MHCI-eluted ligands (proteasome model) or CD8 T cell epitopes (immunoproteasome) and the corresponding C-terminal flanking residues. Predictive performance was evaluated in 5-fold cross-validation experiments. SE: sensitivity; SP: specificity; MCC: Matthew's correlation coefficient; BTR: better than random (Eq. 4)