Fig. 2

Evaluation of the effects of drug treatments on molecular profiles. a Sample collection design of the drug response cohort. Responders and inadequate responders to the drug treatments were defined based on EULAR response criteria. Patients who displayed a good response via the criteria at 24 weeks after the first drug administration were classified as responders; others were classified as inadequate responders. The average DAS28-ESR and sampling timing for each group are shown. b RA probability changes induced by the treatments. RA probability was transformed to log-odds, and the log-odds at week 0 were compared with those at week 24 using the paired t-test (*p < 0.05) for each treatment arm (n = 10 for each drug). c The temporal change in log-odds for being RA during the treatments. The temporal effects of RA odds (n = 10 for each drug) were modeled with B-spline smoothing, in which an individual was treated as a random effect. d Correlation between the model-based assessments of drug effects and the clinical definition of drug response. The treatment effects on RA odds were compared between responders (n = 30) and inadequate responders (n = 22) by Welch's t-test. e The number of variables affected by drug treatments (24 vs 0 weeks). Treatment effect was tested for each drug (n = 10) via limma by taking into account the paired samples. RIN value was included in the regression model for testing transcripts. The criterion for significance was set at a p value <0.05 and FDR <0.05. f Neutrophil and NK cell counts before and after treatment. The asterisk represents a p value <0.05 and FDR <0.05. The upper, center, and lower line of the boxplot indicates 75%, 50%, and 25% quantile, respectively. The upper and lower whisker of the boxplot indicates 75% quantile +1.5 * interquartile range (IQR) and 25% quantile −1.5 * IQR