GSEA and GSVA

The R package “clusterprofiler” (Yu et al., 2012) was utilized to perform GSEA analysis of hub genes with TCGA-PRAD RNA-seq data. Moreover, the “GSVA” (Hänzelmann and Guinney, 2013) R package was used to find the pathways that are mostly associated with the hub genes. In this analysis, 498 PCa samples were divided into two groups (high vs. low expression) based on the median expression of each hub gene. P < 0.01 and log fold change of >0.15 were considered significant. The reference gene sets of GSEA and GSVA, which was called as “c2.cp.kegg.v6.2.symbols.gmt,” were downloaded from the Molecular Signatures Database³.