Fig. 4

Spike pattern analysis of top 20 patterns with most significantly up- or down-regulated probes. Genes that are showing significant up- or down-regulation between infected and control mice were clustered together based on time post-inoculation. Panel a: Top 20 clusters (#1- #20, left Y-axis)) were identified by Functional analysis Heatmap. These clusters were ranked in descending order based on the number of probes (e.g., 2041, right Y-axis) determined as significantly up- or down-regulated at different time post-inoculation (X-axis). The assignment of “0” (gray), “-” (blue), and “+” (red) to certain expression pattern was defined as described in Methods. It is noted that these top 20 clusters were mostly single time point up- or down-regulated in the infected group in comparison to the sham group. Panel b: Number of probes showing up-regulation (red) and down-regulation (blue) at different time post-infection