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)
.