FIGURE 1.

Four distinct transcriptional phases during denervation-induced muscle atrophy. (A) The number of DEGs at different times in TA muscles post nerve injury as compared to control (0 h post sham surgery). (B) SOMs: Color-coded output maps representing the final weight of denervated muscle atrophy. The cluster centroid value is coded with a range of colors from blue (for the lowest expression level) to red (for the highest expression level). (C) Pearson correlation heatmap between different times post nerve injury, as labeled on down and right margins. Arrows indicate three nodal transitions. (D) PCA of DEGs at different times post nerve injury. The percentage of variance captured by principal components (PCs) is shown. (E) Dendrogram of gene expression profiles, created by hierarchical clustering analysis. The three nodal transitions in temporal gene expressions segregate the four distinct transcriptional phases within the period of 28 days post nerve injury, and they were designated as “oxidative stress stage,” “inflammation stage,” “atrophy stage” and “atrophic fibrosis stage,” respectively.