Table 3 Comparison between EpiJen, NetCTL, WAPP and SMM on HIV epitopes, binding to HLA-A*01, HLA-A*02 and HLA-A*03.
From: EpiJen: a server for multistep T cell epitope prediction
| Â | p17 | p24 | protease | RT | integrase | rev | tat | vif | vpr | vpu | gp160 | nef | total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A*01 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 4 |
A*02 | 2 | 9 | 2 | 11 | 3 | 3 | 0 | 3 | 4 | 1 | 20 | 8 | 66 |
A*03 | 2 | 2 | 1 | 9 | 2 | 2 | 1 | 2 | 0 | 0 | 4 | 4 | 29 |
total | 5 | 11 | 3 | 20 | 5 | 6 | 1 | 5 | 4 | 1 | 25 | 13 | 99 |
EpiJen | |||||||||||||
TP | 5 | 7 | 2 | 14 | 2 | 5 | 1 | 3 | 2 | 0 | 14 | 6 | 61 |
FN | 0 | 4 | 1 | 6 | 3 | 1 | 0 | 2 | 2 | 1 | 11 | 7 | 38 |
FP | 16 | 17 | 8 | 42 | 26 | 13 | 4 | 17 | 3 | 4 | 115 | 24 | 289 |
Sensitivity % | 100 | 64 | 67 | 70 | 40 | 83 | 100 | 60 | 50 | 0 | 56 | 46 | 62 |
PPV % | 24 | 29 | 20 | 25 | 7 | 28 | 20 | 15 | 40 | 0 | 11 | 20 | 17 |
NetCTL | |||||||||||||
TP | 4 | 6 | 1 | 10 | 3 | 3 | 1 | 4 | 1 | 0 | 12 | 4 | 49 |
FN | 1 | 5 | 2 | 10 | 2 | 3 | 0 | 1 | 3 | 1 | 13 | 9 | 50 |
FP | 8 | 10 | 6 | 39 | 22 | 5 | 7 | 11 | 4 | 2 | 60 | 14 | 188 |
Sensitivity % | 80 | 55 | 33 | 50 | 60 | 50 | 100 | 80 | 25 | 0 | 48 | 31 | 50 |
PPV % | 33 | 38 | 14 | 20 | 12 | 38 | 13 | 27 | 20 | 0 | 17 | 22 | 21 |
WAPP | |||||||||||||
TP | 2 | 2 | 2 | 7 | 1 | 4 | 0 | 3 | 3 | 0 | 8 | 1 | 33 |
FN | 3 | 9 | 1 | 13 | 4 | 2 | 1 | 2 | 1 | 1 | 17 | 12 | 66 |
FP | 8 | 6 | 4 | 40 | 13 | 6 | 2 | 13 | 0 | 6 | 61 | 7 | 166 |
Sensitivity % | 40 | 18 | 67 | 35 | 20 | 67 | 0 | 60 | 75 | 0 | 32 | 8 | 33 |
PPV % | 20 | 25 | 33 | 15 | 7 | 40 | 0 | 19 | 100 | 0 | 12 | 13 | 17 |
SMM | |||||||||||||
TP | 3 | 6 | 2 | 15 | 5 | 4 | 0 | 3 | 2 | 0 | 14 | 3 | 57 |
FN | 2 | 5 | 1 | 5 | 0 | 2 | 1 | 2 | 2 | 1 | 11 | 10 | 42 |
FP | 15 | 18 | 8 | 41 | 23 | 14 | 5 | 17 | 3 | 4 | 115 | 27 | 290 |
Sensitivity % | 60 | 55 | 67 | 75 | 100 | 67 | 0 | 60 | 50 | 0 | 56 | 23 | 58 |
PPV % | 17 | 25 | 20 | 27 | 18 | 22 | 0 | 15 | 40 | 0 | 11 | 10 | 16 |