Module enrichment in DE, DV, and DW genes was used to assess the effects of selection on network structure. We considered a module “enriched” based on overlap between module genes and DE/DV/DW genes, using Fisher’s exact test with Bonferroni correction for number of modules. The Gorilla algorithm (Eden et al., 2009) was used to provide a visual representation of GO annotation enrichment. To implement a ranking procedure we integrated differential network results at the module and gene summarization level into a comprehensive gene screening procedure. Modules enriched in gene or edge changes were the primary focus of further annotations. At the individual gene level, we focused on module hubs with normalized intramodular connectivity above 0.8 (see Colville et al., 2017; Iancu et al., 2018).
