Skip to main content

Table 4 The proteins included in the reduced datasets identified by RGIFE for the canine proteomics emPAI and ProteinProphet data.

From: A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

Protein ID Protein name Identified from emPAI or ProteinProphet Protein description Known link to cartilage inflammation or OA
MMP-3 matrix-metalloproteinase 3 ProteinProphet and emPAI MMP-3 is a proteolytic enzyme known to degrade components of the ECM, including collagens and cartilage proteoglycans [53]. Found to be down-regulated in late OA [33].
IL-8 interleukin-8 ProteinProphet IL-8 is a chemotactic factor that attracts neutrophils, basophils, and T-cells, but not monocytes. It is also involved in neutrophil activation. It is released from several cell types in response to an inflammatory stimulus [54]. IL-8 is the major chemotactic factor released in response to proinflammatory cytokines in synovial tissues from RA and OA affected joints [34].
TSP1 thrombospondin-1 ProteinProphet Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions [55]. Levels of TSP1 are increased after the onset of OA [35]
APOE apolipoprotein E ProteinProphet APOE mediates the binding, internalization, and catabolism of lipoprotein particles [56]. No known link.
HPLN1 hyaluronan and proteoglycan link protein 1 ProteinProphet Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix [57]. HPLN1 has been associated with OA and osteophyte formation [36].
TPIS triosephosphate isomerase ProteinProphet Catalyses the reaction D-glyceraldehyde 3-phosphate = glycerone phosphate [58]. No known link.
CLUS clusterin emPAI A glycoprotein that functions as extracellular chaperone that prevents aggregation of non-native proteins, which is involved in many diverse biological functions [59]. Higher levels of clusterin have been observed in synovial fluid of advanced primary knee and hip OA patients [37].
FETUA alpha-2-HS-glycoprotein/fetuin-A emPAI Promotes endocytosis, possesses opsonic properties and influences the mineral phase of bone [60]. FETUA levels have been found to decrease as the severity of knee OA increases [38].
POLG Genome polyprotein emPAI Bacterial protein. No known link.
ATPX ATP synthase subunit b' emPAI Bacterial protein. No known link.