Genes associated with SNP outliers and DMRs, and gene ontology
analyses
We investigated whether genomic outliers and DMRs overlapped genes in 5
kb upstream and downstream regions using BEDTools v2.28.0 (Quinlan &
Hall, 2010). Gene ontology analyses were performed with the R package
topGO (Alexa & Rahnenführer, 2009), with GO referenced for the chickenGallus gallus (ggallus_gene_ensembl), to identify potential
statistically enriched genes ontologies among the lists of genes
extracted. In order to take into account hierarchy and non-independence
in GO terms we used the “weight01” algorithm with a “fisher”
statistic (options algorithm=“weight01” andstatistics=“fisher” of the runTest() function). GO terms
were considered significantly enriched when having a weightFisher
< 0.05.