Clustering results using DEPs and DEGs. (A) Heat map for expression of DEGs across the samples. Each lane represents the expression profile of one sample. Result of hierarchical clustering with DEGs is shown at the top of the heat map (UI, Uninfected; AT, Acute; NP, Non-progressive; CN, Chronic). (B) Heat map for co-expressed score of DEPs. (C) Four representative clusters of gene pairs. Of six groups of gene pairs clustered by K-means clustering using Pearson’s correlation between pairs and samples, four groups had relatively different co-expression scores compared with the other stages. The X-axis represents samples, and the Y-axis represents co-expression score. The top 10 GO terms related to biological processes are listed in descending order of p-values.