Figure 3.

Distribution of biological process genes and gene sets across the synovial tissue phenotypes. (A) Heatmap of expression of selected genes in lymphoid (red), myeloid (purple) and fibroid (green) patient subgroups. Patient-sample clusters are supervised by prior phenotype assignment, and genes are distributed by unsupervised clustering. (B-G) Distribution of biological processes for each synovial phenotype (L = lymphoid, M = myeloid, X = low inflammatory, F = fibroid) was assessed using predefined gene sets to interrogate the respective microarray datasets. Gene sets reflecting B cells (B), T cells (C), M1 classically activated monocytes (D), genes induced by TNFα (E), M2 alternatively activated monocytes (F) and angiogenesis (G). Each subgroup was compared to all other groups using the f-test, and significant Benjamini-Hochberg-corrected P-values for a group compared with all other groups are indicated (*P ≤0.05, **P ≤0.01, ***P ≤0.001) for subgroups with positive t-statistic values.

Dennis et al. Arthritis Research & Therapy 2014 16:R90   doi:10.1186/ar4555
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