Fig. 1

Pharmacodynamic effects of anti-TNF treatment in gene expression, proteomics, and CBC data. a Gene expression profiles show statistically significant differences (after FDR correction) between the month 3 and baseline samples in C1 (pink), but not in C2 (blue). b Scatterplot of mean MO3-BL differences in gene expression levels for cohort 1 (x-axis) and cohort 2 (y-axis). Color labels indicate CD cell surface markers up- (orange) or downregulated (blue) in both cohorts. c 2D density contours of genome-wide mean MO3-BL gene expression differences (y-axis) and log-fold differences in expression levels between neutrophils and the rest of cell types in NCBI-GEO dataset GSE60424 (x-axis): genes overexpressed in neutrophils are downregulated at 3 months in both cohorts. d Average differences (%) and 95% confidence intervals on the neutrophils/WBC ratios in CBC metrics for EULAR-GR and EULAR-NR at BL and MO3. e Distribution of treatment (MO3-BL) effect p values in plasma proteomics analysis manifests an increase in small p values for both cohorts. f Average MO3-BL differences in plasma protein levels show a positive correlation between two cohorts infrequently observed upon permutation. Labels indicate proteins with BH-FDR < 20% in both cohorts