Table 1 Descriptions of datasets analysed, including both proteomic and transcriptomic. Those prefixed 'GSE' were from NCBI GEO and those prefixed 'E-GEOD' were from ArrayExpress.

emPAI canine

23

178

4

Articular cartilage dataset treated with IL-1β to stimulate inflammation. Some samples were also treated with carprofen, a non-steroidal anti-inflammatory drug. Other samples were treated with carprofen only or nothing, as a control. The emPAI dataset includes emPAI label-free quantitation to compare protein quantities across samples, for the proteins with Mascot scores above 30. The ProteinProphet dataset includes a probability for each protein identified in each sample indicating how likely it is to be present in the sample.

ProteinProphet canine

23

1322

4

Transcriptomics datasets:

GSE36700

25

54675

5

Comparison between gene expression in synovial biopsies from patients with OA, RA, Systemic Lupus Erythematosus (SLE), seronegative arthritis (SA), and microcrystalline arthritis (MIC) [48]

GSE3698

48

17048

3

Comparison between OA, RA & Pigmented villonodular synovitis (VS), a rare group of lesions with morphological features suggesting an inflammatory as well as a neoplastic nature. All three diseases result in a progressive destruction of affected joints and remain a diagnostic difficulty because of nonspecific symptoms. Tissue samples obtained from knee surgery [49]

E-GEOD-12021

31

22284

3

Gene expression variances were tested in synovial membrane samples of RA patients, OA patients, and normal controls [50]

E-GEOD-29746

31

44397

3

Comparison of gene expression between two pathological groups of human synovial fibroblasts (SF) from RA and OA synovial tissues with normal SF from healthy individuals [51]

E-GEOD-27390

19

54675

2

Gene expression profiling of bone marrow-derived mononuclear cells from patients with RA vs. OA [52]