WGCNA allows for the generation of gene modules that are related by their co-expression patterns. Studies employing WGCNA have found that modules organized by co-expression patterns are enriched for biologically relevant functions [49–51]. Thus, the mRNA modules significantly correlated with AD were assessed for enrichment of cellular process and biological functional categories using the gene set enrichment analysis (GSEA) software. Gene lists for each module were generated by ranking all 4571 differentially expressed transcripts according to their MM in each of the six significant mRNA modules, which was achieved by correlating individual gene expression values to the ME of each of the six significant modules (as previously described) [52]. To assess for enrichment of cellular processes and functional categories, all transcripts from the mRNA modules were collapsed into unique, functionally annotated genes by GSEA, resulting in 3742 unique gene symbols. Using the default parameters in GSEA, we identified 364 a priori gene sets significantly enriched (FDR≤ 0.10) within the six MM ranked gene lists. Of these, 117 a priori gene sets were enriched in multiple (≥2) modules. Interestingly, no a
