It was found that the patients with atherosclerosis or ischemic stroke exhibited significant difference in gene profiling and 9 common genes were found in GES16561 and GES100927 including AQP9, CD2, CD3D, CD8A, FCGR3A, ITGAM, KCNJ15, MMP9, and NPL, suggesting that the DEGs were related to the progression of ACI. The gene discussed is MMP9; the disease is atherosclerosis.