There were twelve matrix metalloproteinases in each dataset, most were unaffected but MMP9 (−4.95 and −5.37 fold) was repressed in both M and P. The inflammation pathways ‘LXR/RXR Activation’, ‘Granulocyte Adhesion and Diapedesis’, ‘Acute Phase Response’ and ‘Role of Osteoblasts, Osteoclasts and Chondrocytes in Rheumatoid Arthritis’ were also common to the two datasets. The gene discussed is MMP9; the disease is rheumatoid arthritis.