Table 4. Predictive analysis of changes in protease activity associated with peptides differentially regulated in RA 1.
| Protease | occ(up)[N(up) = 67] | occ(down)[N(down) = 64] | % frequency(up) | % frequency(down) | % frequencydifference ratio | Frequencyscores |
| Kallikrein 6 | 7 | 1 | 10.5 | 1.6 | 74.0 | 443.9 |
| Plasminogen | 8 | 2 | 11.9 | 3.1 | 58.5 | 351.1 |
| Cathepsin B | 38 | 55 | 56.7 | 85.9 | 20.5 | −348.2 |
| MMP9 | 58 | 78 | 86.6 | 121.9 | 16.9 | −338.8 |
| MMP8 | 33 | 48 | 49.3 | 75.0 | 20.7 | −310.8 |
| MMP13 | 34 | 49 | 50.8 | 76.6 | 20.3 | −304.2 |
| MMP3 | 35 | 50 | 52.2 | 78.1 | 19.9 | −297.9 |
| Prolyl endopeptidase | 10 | 4 | 14.9 | 6.3 | 41.0 | 245.8 |
| ADAMTS4 | 6 | 12 | 9.0 | 18.8 | 35.4 | −212.1 |
| Kallikrein 4 | 6 | 2 | 9.0 | 3.1 | 48.3 | 193.1 |
| Granzyme A | 11 | 6 | 16.4 | 9.4 | 27.3 | 136.5 |
| KLK3 | 0 | 1 | 0.0 | 1.6 | 100.0 | −100.0 |
| MMP20 | 7 | 4 | 10.5 | 6.3 | 25.1 | 75.4 |
| Cathepsin L1 | 24 | 18 | 35.8 | 28.1 | 12.0 | 72.2 |
| Thimet oligopeptidase | 2 | 4 | 3.0 | 6.3 | 35.4 | −70.7 |
| MMP25 | 4 | 2 | 6.0 | 3.1 | 31.3 | 62.6 |
| Thrombin | 4 | 2 | 6.0 | 3.1 | 31.3 | 62.6 |
| Signal peptidase complex catalytic subunit | 8 | 11 | 11.9 | 17.2 | 18.0 | −54.0 |
| MMP14 | 30 | 35 | 44.8 | 54.7 | 10.0 | −49.8 |
| Kallikrein 2 | 5 | 3 | 7.5 | 4.7 | 22.8 | 45.7 |
| MMP12 | 63 | 69 | 94.0 | 107.8 | 6.8 | −41.0 |
| MMP1 | 26 | 30 | 38.8 | 46.9 | 9.4 | −37.7 |
| Cathepsin S | 15 | 12 | 22.4 | 18.8 | 8.8 | 26.5 |
| Triptidyl-peptidase 1 | 3 | 4 | 4.5 | 6.3 | 16.5 | −16.5 |
| ADAMTS5 | 18 | 20 | 26.9 | 31.3 | 7.5 | −15.1 |
| Kallikrein 5 | 4 | 3 | 6.0 | 4.7 | 12.0 | 12.0 |
| MMP2 | 28 | 30 | 41.8 | 46.9 | 5.7 | −11.5 |
| Cathepsin K | 16 | 14 | 23.9 | 21.9 | 4.4 | 8.8 |
| MMP7 | 42 | 43 | 62.7 | 67.2 | 3.5 | −3.5 |
| Meprin A | 38 | 36 | 56.7 | 56.3 | 0.4 | 0.8 |
| Calpain 2 | 10 | 10 | 14.9 | 15.6 | 2.3 | 0.0 |
| Neprilysin | 10 | 10 | 14.9 | 15.6 | 2.3 | 0.0 |
1
Frequency distribution analysis based on all peptides (n = 131).
Mathematical calculations are based on the following parameter and calculations:
occ(up) = Sum of all occurrences for each individual protease in the up-regulated peptides,
occ(down) = Sum of all occurrences for each individual protease in the down-regulated peptides,
N(up) = Total number of peptides being up-regulated,
N(down) = Total number of peptides being down-regulated,
% frequency(up) = (occ(up)/N(up)) * 100.
% frequency(down) = (occ(down)/N(down)) * 100.
% frequency difference ratio = | ((freq%(up) − freq%(down))/(freq%(up)+freq%(down)) * 100 |.
Frequency scores = %freq * (occ(up)-occ(down)).