Extended Data Fig. 3: Influence of immune cells on consensusclusters.

a-d, Volcano plots showing differential gene expression analysis using DESeq2 comparing consensuscluster 1 and 2 of patients treated with rituximab (left) or tocilizumab (right). While a and b were analyzed without covariates, c and d were adjusted for principal component (PC1). Comparison between groups were tested for significance using Wald test and multiple testing was corrected for with Storey’s q value (q < 0.05 = significant, shown in blue). Positive log2fold changes represent upregulation in consensuscluster 2, negative log2fold changes represents upregulation in consensuscluster 1. e, Correlation plot highlighting relation between PC1, histology markers and genes involved in the mode of action of RTX and TOC. Positive correlation is shown in blue while red would indicate negative correlation. For all correlations without significance, the p-value is shown. f,g, Volcano plots of DEGs using DESeq2 comparing CDAI50% responders versus non responders to rituximab (f) and tocilizumab (g) after adjustment for principal component 1. Comparison between groups using Wald test and correcting for multiple testing Storey’s q value (q < 0.05 = significant, shown in blue). Positive values represent upregulation in responders and negative values downregulation compared to non-responders.