Fig. 2

The most significantly upregulated genes in brain microvessels after LPS are related to inflammation in all diets, while ECM genes are among the most significantly downregulated genes in standard and n-6 diets only. (A) Venn diagram of all genes regulated by LPS (adjusted p < 0.05) within each diet. (B) Heatmap of normalized counts of all genes regulated by LPS across all diets (1214 genes in total) sorted using hierarchical clustering. Each column refers to one microvessel sample and each row shows level of a specific gene. Numbers of transcripts for each gene were normalized over all samples using z-score normalization and is shown using a colour scheme based on z-score distribution from − 2 to 2. (C) Scatter plot (Volcano plot) of p-value (y-axis) versus difference of means (x-axis) of all genes within each diet. Significantly regulated genes are coloured blue (downregulated) or red (upregulated). Note the higher number of downregulated genes in the standard diet than in the n-3 or n-6 diets. Genes with high magnitude of change and low p-value have been highlighted