*2.6. Over-Representation Analysis (ORA)*

The "kegga" function under the "goana" package in R utilized the user-supplied GO slim assignment and InterPro classification from RGAP 7 independently in the form of data.frame annotation alongside the multiple gene lists generated in each module. Gene.pathway was the data.frame linking genes to pathways and pathway.names was the data.frame giving full names of pathways. The universe was the vector specifying the set of unique gene identifiers used in WGCNA to be the background and not the whole genome. Finally, GO slim terms, and InterPro protein families and domains were called significantly over-represented in the gene set if the *p-*value is < 0.05.
