Our study has demonstrated that significant number of differential genes in SLE was involved in IFN, TLR signaling pathways and inflammatory cytokines. The enrichment of differential genes has been associated with aberrant DNA methylation, which may be relevant to the pathogenesis of SLE. Our observations laid the groundwork for further diagnostic and mechanistic studies of SLE and LN. We performed whole genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN+) and 15 without LN (SLE LN-), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum pro-inflammatory cytokines were quantified using Bio-plex human cytokine 27-plex assay.