Basic workflow of this study.

(A)We use microarray experiments to study differential gene expressions under specific disease conditions. (B.1)The DEGs are mapped to PPI networks using STRING database to get time-stamped PPI networks for every mouse-prion models. (B.2)Protein networks are used to identify potential disease related genes. (B.3)The identified shared DEGs are then used to identify genes potentially participating in crosstalk. These potential crosstalk genes are then mapped to KEGG database to identify a consensus bow-tie network. (C)Mathematical modeling of the identified bow-tie network using ordinary differential equations. (D) Prediction of the activities of the network components during disease condition. (E)Validation of predicted differential gene expression by comparing it with the microarray results. *The microarray experiments were performed in Hwang et al. [5].