Pathway analyses derived from differential expression analysis on the three different clinical indexes and the presence of lupus nephritis, a type of kidney complication caused by SLE, across the immune cell types showed enrichment of pathways in CD4 and CD14 for lupus severity index and SLICC score while SLEDAI score was enriched in CD4 only (Supplementary Fig. 6). Here, CD4 is linked to lupus nephritis.