The most prominent functional categories included ribosomal genes, genes involved in skeletal muscle contraction, actin, cytoskeleton and protein biosynthesis.
The prominent functional categories for both induced and repressed genes were related to metabolic process, followed by cellular process, response stimulus, biological regulation, and localization.
The third most prominent functional category contained genes involved in production and recycling of amino acids.
The most prominent functional category identified was for stress-related genes.
The most prominent functional category in group C contigs up-regulated in both genotypes, with a higher expression in the resistant genotype was "cell wall".
Protein metabolism was the second most prominent functional category and was dominated by the subcategory of biosynthesis (69%), followed by folding (16%), secretion (8%), and degradation (6%).
Another prominent functional category, common to the Tiers 0 3, was MHC binding, receptor binding, ubiquitin targeting and other forms of protein binding mediated by proteasome subunits, cytoskeleton and chaperones (ubiquitin-conjugating enzyme E2N; proteintein (Cdc42/Rac -activated kinase 1; thymus Cdc42/Rac -activatedctin β; actin γ1).
The prominent genes for one or two organs were further classified into 4 functional categories: function unclear, cellular location, molecular function, and biological process, using ontology annotations from Rat Genome Database and Gene Ontology.
Functional categories prominent in healthy controls were mostly related to nutrient metabolism.
The main functional categories of prominent genes were summarized in Additional file 4 (Supplementary Table E3) for one organ and in Additional file 5 (Supplementary Table E4) for two organs.
In cellular component category, six prominent functional gene classes, including the cellular-component related genes, nucleus related genes, mitochondrial proton-transporting ATP synthase complex related genes, cytoplasm related genes, cell plate related genes and cytoskeleton related genes, were over-represented in four comparison groups (Fig. 5b).
