SHH and rheumatoid arthritis: Ingenuity Pathways Analysis implicated biologically relevant pathways in the gene expression difference between IDZ and RZ, including Role of Osteoblasts, Osteoclasts and Chondrocytes in Rheumatoid Arthritis that was more active in IDZ as well as sonic hedgehog (SHH) and bone morphogenetic protein (BMP) signaling pathways that were more active in RZ (Table 5 and Table S4 in File S1).