The intersection of the top 25 pathways for seropositive RA, seronegative RA and PIA pathway analysis revealed 8 common pathways: the endosomal/vacuolar pathway, the antigen presentation: folding, assembly and peptide loading of class I MHC, interferon alpha/beta signaling, the ER-Phagosome pathway, the interferon pathway, antigen processing–cross presentation, interferon gamma signaling and cytokine signaling in the immune system with preserved significance after BH-correction (Supplementary Materials Tables S1–S3). This evidence concerns the gene IFNG and rheumatoid arthritis.