Functional Annotation Analyses

The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7b (Huang et al., 2008) was used to determine pathways and processes of major biological significance and importance through the Functional Annotation Cluster (FAC) tool based on the Gene Ontology (GO) annotation function. DAVID FAC analysis was performed with the gene lists obtained after SAM analysis. Medium stringency EASE score parameters were selected to indicate confident enrichment scores of functional significance and importance of the given pathways and processes investigated. An enrichment score of 1.3 was employed as the threshold for cluster significance. The ClueGO plug-in (Bindea et al. 2009) and Cytoscape program (Shannon et al., 2003) were used to group genes according to the similarity of the biological processes in which they are involved. The relationships between the n−3 PUFA series in muscle and gene expression in liver were visualized using the Metscape plugin (Karnovsky et al., 2012) in Cytoscape (Shanon et al., 2003). Thirty significant genes (out of 96) and nine (out of 13) significant compounds were mapped to KEGG IDs. The file containing the list of genes and metabolites, their fold change and P-values was loaded in Metscape to generate a compound-gene network.