WGCNA(Weighted gene co-expression network analysis) is a widely used data mining method that includes functions for network construction, module detection, gene selection, calculations of topological properties, visualization, and interfacing with external software. In this platform, WGCNA is used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures.

When possible (study not completely confounded with treatment), batch effects due to studies were adjusted using SVA. The final step is enrichment analysis based on each modules.