Fig. 3

Weighted Gene Coexpression Network Analysis (WGCNA). a Cluster dendrogram built based on 1614 DEGs in WGCNA. All modules and merged modules with a module dissimilarity threshold of 0.25 were shown in upper and down panel, respectively. b Heatmap showing correlations between module eigengenes and each of the four states. The color scale indicates the strength of correlation. Number of genes included in each module was shown in the bar plot right; c-e Results of protein-protein interaction (PPI) network analysis on DEGs in three WGCNA modules (TP-M9, TP-M10 and AS-M1 modules; c, d and e). Size of nodes indicates module membership values (MM) of specific DEGs in corresponding WGCNA modules. Size of the label indicates the mean expression level (log₂CPM) across the samples. Proteins discussed in Results are cycled with red color. Edge transparency indicates the interaction score between two proteins (less transparent stronger correlation of the two proteins)