Functional gene ontology analysis of the genes where SLE-specific differential DNA methylation was found, revealed beside an enrichment for broader functions of hemostasis and innate immunity, an overrepresentation of genes involved in induction and regulation of apoptotic processes and NFκB activation with a key role for FADD and CASP-8 and -9. This evidence concerns the gene NFKB1 and systemic lupus erythematosus.