Although IFN-Score-A and IFN-Score-B shared several key ISGs, specific genes for IFN-Score-A were mostly typical ISGs, i.e., IFIT1, IFI27, RSAD2, IFI44L, IRF7, ISG15, and XAF1. On the other hand, specific genes for IFN-Score-B were LAMP3, UNC93B1, SP100, IFI16, IFIH1, PHF11, and BST2. IFN-Score-A differentiated SLE from both rheumatoid arthritis (RA) and healthy controls (HC), while IFN-Score-B differentiated SLE and RA from HC. Here, PHF11 is linked to rheumatoid arthritis.