Gene ontology enrichment analyses
Gene ontology enrichment analyses were performed with topGO (Alexa, A.
et al., 2006), using Drosophila melanogaster orthologs of honey
bee genes converted via a one-to-one reciprocal best hit BLAST (Table
S15). We focused our assessment (Tables 3-4) on the more specific and
highly enriched terms through sorting each resulting GO term list by
percent coverage (defined as the proportion of genes associated with a
GO term represented among the differentially expressed genes in each
phenotype contrast) and selecting the top quartile, and then by GO term
rank (defined as the number of child terms per GO term) and selecting
the bottom quartile. Thus, Tables 3-4 represent the significantly
enriched GO categories that had the largest proportion of DEGs and the
most specific biological functions.