To characterize gene expression aberrancies in CD4+ T cells that drive disease pathogenesis of SSc, we performed genome-wide RNA expression analysis and found that a total 3929 genes displayed differential expression (differentially expressed genes (DEGs)) between HD and SSc, of which 1949 and 1980 were down- and upregulated, respectively (Fig. 3a, b; Additional file 7: Table S5). This evidence concerns the gene CD4 and systemic sclerosis.