Fig. 3

Functional annotation of genes validated stronger ECM gene response in standard and n-6 diet, additionally highlighting downregulation of cell cycle pathways only in standard diet. (A) Graphical pathway maps from overrepresentation analysis of all genes regulated by LPS within each diet created using the Reactome browser (adjusted p < 0.05; DeSeq). Yellow represents specific enrichment. Enrichment of pathways annotated to immune system (innate- and adaptive-immune system as well as cytokine response) is present in all three diets. Note high annotation to cell cycle and extracellular matrix (ECM) organisation pathways in the standard diet. The n-3 and n-6 diet show no enrichment of cell cycle pathways and n-3 diet shows least enrichment of ECM pathways. (B) PCA plots of individual genes annotated to immune system (upper panel), cell cycle (middle panel), and ECM (lower panel) regulated by LPS within each diet. Variables are colour-coded according to distance between them rendering upregulated genes red and downregulated genes blue. Numbers of regulated genes are stated in upper right corner out of all analysed genes for each process (in brackets)