Additional file 7: Figure S4.

B cell, M1 classically activated monocyte, and fibroid gene modules capture synovial tissue transcriptional heterogeneity in additional rheumatoid arthritis (RA) patient cohorts. (A) Scatter plot of the training cohort of 49 patient synovial samples projected in gene set space of the B cell (x-axis) and M1 monocyte (y-axis) biological modules. Samples are colored according to their cluster assignments in Figure 1 (red = lymphoid, purple = myeloid, green = fibroid, grey = low inflammatory). Filled circles indicate samples with histologic aggregates and empty circles indicate samples lacking aggregates. Scatter plot of the same 49 RA patients projected in gene set space of the B cell (x-axis) and M1 monocyte (y-axis) biological modules, and samples are also colored according to their respective fibroid gene set scores as indicated by the color bar. (C) Scatter plot of 33 previously unanalyzed patient samples from a parallel Michigan RA cohort projected in gene-set space of the B cell (x-axis) and M1 monocyte (y-axis) biological modules. Samples are colored according to their respective fibroid gene-set scores as indicated by the color bar. (D) Scatter plot of a publicly available cohort of 62 RA histologically characterized patients (GSE21537) projected in gene-set space of the B cell (x-axis) and M1 monocyte (y-axis) biological modules. Samples are colored according to their respective fibroid gene-set scores as indicated by the color bar.

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