Functional analysis of the differentially expressed genes: gene ontology analysis
To identify potential biological functions that were overrepresented in the expressed genes, the differentially expressed up- and downregulated transcripts were extracted and tested for enriched Gene Ontology (GO) terms with the R package topGO 2.30.1 (Alexa et al. 2006) for biological processes (BP). The GO-terms were extracted from the stickleback genome in Ensembl (n=1829 GO-terms that were linked to the 16.111 transcripts). Checking for significance, a classical Fisher test on GO-terms with 10 or more annotated genes were used as a cut-off. The top 10 results are presented as tables on sorted weighted values.