Figure 3.

Overlapping transcriptomic effects of five DMARDs on paired pre/post-treatment RA synovial biopsies. (A) Correlation matrix showing Pearson’s r between mean Log₂FCs induced by pairs of DMARDs. Cells show values for the differentially expressed genes of each DMARD (Columns: “DEG”), vs. the modulation of these same transcripts by each of the other DMARDs (Rows). “DEG ABA” = 5824 transcripts significantly modulated by ABA between W0 and W16, “DEG TCZ” = 6726 transcripts, “DEG RTX” = 4577 transcripts, “DEG MTX” = 1228 transcripts, “DEG ADA” = 3383 transcripts. p < 10e^-8 for all correlations. (B) Circos plot showing overlap between genes downregulated by each DMARD, and all other DMARDs. Each purple line joins a pair of shared genes. For each DMARD, the fraction of unique genes downregulated by at least one other DMARD is indicated. (C) Top 20 pathways identified by enrichment analysis of 227 genes downregulated by ≥3/5 DMARDs. Full pathway IDs: *Leukocyte activation involved in immune response, **Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. (D) Transcription factor enrichment analysis of 227 genes downregulated by ≥3/5 DMARDs.