WGCNA Analysis

The co-expression network analysis was performed using Weighted Gene Co-Expression Network Analysis (WGCNA, version 1.69) (Langfelder and Horvath, 2008). The TPM values of PCGs were used as input for module detection. First, the soft threshold for network construction was selected, which was 6 here. The soft threshold made the adjacency matrix to be the continuous value between 1 and 20, so that the constructed network was conformed to be the power-law distribution and was closer to the real biological network state. Second, the scale-free network was constructed using blockwiseModules function, followed by the module partition analysis to identify gene co-expression modules, which could group genes with similar patterns of expression. The modules were defined by cutting the clustering tree into branches using a dynamic tree-cutting algorithm and assigned to different colors for visualization. Finally, we obtained three modules containing less than 1000 member genes. The co-expression network of each module was exported using exportNetworkToCytoscape function and further visualized by Cytoscape (version 3.6.0) (Shannon et al., 2003).