Fig. 3

Heatmap of the top 500 differentially expressed genes. Differentially expressed genes (DEGs) between the 6 study groups were determined using linear mixed-effects models treating subjects as a random effect. For the top 500 DEGs (all with false discovery rate < 0.05), the scaled signal intensities (z-scores) are visualized, with blue indicating low expression and red indicating high expression. The genes (rows) were ordered by hierarchical clustering, and 8 gene clusters could be defined (shown by the colored bars on the left). The light and dark purple bars at the bottom indicate whether the blood samples were taken before or following the administration of alemtuzumab or cladribine. Paired B samples and F samples of an annual treatment course (represented by the green bars at the bottom) are always arranged in the same order. The samples and genes in the columns and rows are specified in Additional files 2 and 4, respectively. IRT = immune reconstitution therapy, PPMS = primary progressive multiple sclerosis