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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)