The steps for constructing miRNA co-expression modules were as described above (with a few differences). After generating the signed similarity matrix, a β = 5 was chosen to generate the adjacency matrix. A TOM and dissimilarity measure was calculated as previously described and a minimum module size of five miRNA genes was chosen. Five was chosen as the minimum module size for the miRNA genes due to the smaller size of the miRNA transcriptome relative to the mRNA transcriptome. The default minimum module merge height of 0.8 was retained. After modules were defined, MEs were calculated and correlated to AD case-status and demographics, and all confounded modules were removed from subsequent analysis.
