Next we performed differential expression analysis to determine the genes that are regulated by each PPAR agonist in the amygdala, PFC and liver. The top-tables (Tables S1–S3) and the number of differentially expressed genes (Table 1) are shown. Fold changes after feno and tesa treatment are modest in brain relative to those in liver. Fold changes after beza treatment are similar across tissues (Table S4). Note that each Illumina ID maps to only one gene, but one gene can map to several Illumina IDs. Thus, it is possible to have the same gene both up- and down-regulated. This could indicate differential regulation of splice-variants or reflect false positives that are expected in whole-genome analyses. In some cases, the number of unique genes in the up- and down-regulated groups is thus higher than the total number of unique genes in the top-table.
