Volcano plots displaying differential expression. The y axis corresponds to the negative false discovery rate on a log10 scale. The x axis displays the M value (log2 fold change). Differential expression (proportion of false positives < 0.025): (a) between TNF-positive patients and nonresponders (685 differentially expressed (DE) genes) before treatment, (b) before and after treatment in the good responders (115 DE genes), (c) before and after treatment in the moderate responders (0 DE genes), (d) due to treatment in the nonresponders (no DE genes), (e) before and after treatment in all patients (974 DE genes), and (f) before and after treatment in the TNF-positive group of patients (1058 DE genes). TNF-α is highlighted in (e) and (f). FDR, false discovery rate.