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Table 5 The ten mammalian proteins found most frequently in rules for each of the three classes, not including the default control class, from the ProteinProphet and emPAI combined dataset

From: Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning

IL-1β Carprofen IL-1β and Carprofen
Triosephosphate isomerase (19.8) PP Apolipoprotein E (13.7) PP interleukin 8 (33.8) emPAI
Albumin (10) emPAI interleukin 8 (10.8) emPAI interleukin 8 (31) PP
Triosephosphate isomerase (9.3) emPAI interleukin 8 (9.9) PP Clusterin (5.8) emPAI
Matrix metalloproteinase 3 (7.6) PP Matrix gla protein (9.3) PP Matrix metalloproteinase 3 (5.7) PP
Thrombospondin 1 (6.2) PP Hyaluronan and proteoglycan link protein 1 (8.4) PP Thrombospondin-3 (2.4) emPAI
Serum amyloid A protein (3.5) emPAI Fibromodulin (7.4) emPAI Matrix metalloproteinase 3 (2.2) emPAI
Matrix metalloproteinase 3 (3.4) emPAI Transmembrane protein PVRIG (4.6) PP Ribonuclease 4 (1.9) PP
Enolase B (3) emPAI Matrix gla protein (3.2) emPAI Ribonuclease 4 (1.7) emPAI
Keratin (2.5) emPAI Hyaluronan and proteoglycan link protein 1 (2.3) emPAI Cartilage intermediate layer protein 1 (1) emPAI
Enolase A (2.4) emPAI Clusterin (2) emPAI Lumican (1) emPAI
  1. The percentage of rules each protein was used in is shown in brackets. Alongside the proteins the table reports whether the rules were using the protein with its ProteinProphet probability (PP) or emPAI score.