In the brain, significantly altered proteins by EV71 infection participated primarily in complement and coagulation cascades (Serpina1c, C1qb, Fga, C1qa, Kng1, Fgb, Serpinf2, FB, Serpinc1, C4b, and Fgg), infectious diseases (C1qb, FB, Fgg, C1qa, C4b, Tapbp, H2-K1, H2-D1, Srpk1, Srsf5, Syk, STAT1, STAT2, and ISG15), antigen processing and presentation (Tapbp, H2-K1, H2-D1, and Cathepsin S), nitrogen metabolism (Ca5b, Ca4, and Glul), cell adhesion molecules (Ptprc, H2-K1, H2-D1, Cldn3, and CD99), and platelet activation (Mylk2, Fgb, Syk, Fga, and Fgg) (Figures 4A,C and Supplementary Table 5). Here, CD99 is linked to infectious disease.