Weighted Correlation Network Analysis

A weighted correlation network analysis (WGCNA) can be used find phenotype-associated gene modules (Langfelder and Horvath, 2008; Li et al., 2019). RNA-seq data in TPM format were used as the input for a WGCNA. Twelve was set as the soft power threshold to construct a network that simultaneously satisfied a scale-free topology and high connectivity. Pearson correlation coefficients for the relationships between ssGSEA scores and gene modules were calculated. The correlations between the gene significance value and module membership of genes in a module were explored by a Pearson correlation analysis.