Comparison of microarray results with the numerical simulations of the proposed model.

(A) We use constant input signals to observe the behavior of some of the network components of the identified bow-tie signaling network structure. The magnitude of these signals corresponds to the amount of signals of network components Tyrobp, Gnai2, Ifitm1, Jak1, Fcgr2b, and Csf1r, as shown by their differential expressions in the works of Hwang et al. [5]. For most of the mouse-prion combination models, the differential expression pattern of these input gene components are approximately similar. (B) The output signals show the behavior of some of the network components when we apply constant input signals corresponding to the diseased state. (C) Differential expression pattern of the output network components corresponding to the mouse-prion model B6I-301V. This result is taken from the microarray results of the work carried out in Hwang et al. Plots of differential expression of these genes corresponding to other mouse-prion models is given in Figure E in S1 File. (D) Model predictions of the differential expression pattern of the same network components (Fos, Bcl2l1, Ikbkg, Foxo3, and Gsk3b).