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.