Enriched pathways related to CKD stages 3–5 mainly included the apoptosis signaling pathway, T cell receptor (TCR) signaling pathway, PI3K-AKT signaling pathway, hypoxia inducible factor-1 (HIF-1) signaling pathway, Toll-like receptor (TLR) signaling pathway, and TNF signaling pathway. This evidence concerns the gene TNF and chronic kidney disease.