Functional categorization of methylated and unmethylated genes based on Gene Ontology (GO) classification. GO terms were assigned to honey bee predicted proteins using the corresponding GO terms of their BLASTP hits in the RefSeq Drosophila protein database. If the best hit did not have any associated GO terms, the best subsequent hit with associated GO terms was used and no GO terms were assigned to honey bee proteins that did not have any GO annotated hit with an e-value smaller than 1e-5. For illustration purposes only molecular function level 3 ontology terms (where Level 0 = root = Gene_ontology) were selected and grouped into larger categories. See additional file 4 for more details.