Network analysis and module detection
Network analysis identifies gene sets among different subtypes that interact together and are concordantly expressed. The Weighted gene co-expression network analysis (WGCNA) package constructed the gene network and determined modules to identify the function of candidate genes using all 93 samples . After highly co-expressed genes were clustered into co-expressed modules, the module-trait association for all genes was used by topological analysis to generate gene dendrograms to identify modules . Then, the top 10 GO enrichment pathways for each module were identified using the GO enrichment analysis function. Finally, network visualization and functional analysis were performed using Cytoscape software version 3.9.1 (http://www.cytoscape.org) .