Fig. 2.

Expression patterns and enrichment of diet DEGs. A The top 20 most significant (BH-adjusted p ≤ 2.37 × 10⁻⁸) diet DE genes’ average Z scores of median robust multi-array average (RMA) normalized gene expression for each CC strain on either the high-protein (HP) or high-fat high-sucrose (HS) diet shown ordered from top to bottom by level of gene expression on the HP diet (highest to lowest). The genes’ average Z scores for each CC strain and diet are clustered by Euclidean distance on the x-axis. ‡Denotes genes also differentially expressed by strain. *Indicates genes with human homologs found in the GWAS catalog to be associated with at least one obesity-related trait. Annotation and limma results are shown for all diet DEGs in Supplementary Table 3, Additional file 2. Limma analysis of microarray data revealed genes differentially expressed by diet showing significant enrichment (p adj < 0.05) for B KEGG (20 total), C GO biological pathways (105 total), D GO cellular components (45 total), and E GO molecular functions (37 total). Pathways are ordered from top to bottom by significance (highest to lowest) and colored by gene richness. The top 10 enrichments for each ontology category were all upregulated on the HP diet, except for the GO cellular component and “integral component of membrane,” which was downregulated. All significant enrichment terms and enrichment analysis results are shown in Supplementary Table 4, Additional file 2