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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.

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

Dataset No. of samples No. of genes No. of classes Description
Proteomics datasets:
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]