Figure 3.

Searching for cell type specific gene-patterns identified a dominance of monocyte/macrophage infiltration in RA-ST and of synovial fibroblasts in OA-ST. In total, 38 reference transcriptomes (C and F) were applied for analysis of up-regulated probe-sets in RA-ST (n = 1010) (A) and OA-ST (n = 1009) (D). These included: synovial fibroblasts (SFbl) (n = 4, 2 from RA and 2 from OA patients; dark blue), endothelial cells (EC) (n = 4; light blue), platelets (Plt) (n = 3; cyan), CD19⁺B cells (n = 3; green), CD4⁺T cells (n = 3; yellow), CD8⁺T cells (n = 3; yellow), CD56⁺NK cells (n = 3; yellow), CD1⁺DC (n = 3; red), CD14⁺ monocytes (n = 3; red), macrophages (n = 3; differentiated for 3 days from blood monocytes of healthy donors; dark red), macrophages isolated from synovial fluid of RA patients (n = 3; dark red) and CD15⁺ granulocytes (n = 3; pink). The overview of reference transcriptomes is provided in supplementary table 4. Co-expression matrices (B) and (E) were generated by correlating expression of the 1010 and 1009 probe-sets in the reference transcriptomes C and F, respectively. These matrices of correlation coefficients were hierarchically clustered to group co-expressed genes for pattern search in the reference transcriptomes. This order of genes was applied to sort probe-sets in RA-ST and OA-ST (A and D) and in reference transcriptomes (C and F). This alignment identified the patterns, which were characteristic for different cell types.