Fig. 5

Gene expression profiles of selected genes in inflammation pathways. All genes in heat map were present in cluster 4 and found in the NF-kB signaling pathway, cytokine-cytokine receptor interaction, and/or chemokine signaling KEGG pathways. (a) Selected genes were clustered based on molecule functions: cytokines (sky blue), chemokines (yellow green), receptors (pink), NF-kB signaling (brown). Quantile normalized TPM plus 0.1 were transformed between −1 and 1 to present high (red) and low (blue) expression level during time-course across four genotypes for each gene. (b) Schematic of the NF-kB pathway with genes present in heat map colored accordingly. (c) RT-PCR analysis on a subset of genes to validate the RNA-seq dataset. For each gene, 3 samples, two from the RNA-seq dataset and an additional sample not analyzed by RNA-seq, were analyzed for each genotype at ages 5 (left) and 10 months (right). Bars represent group mean expression +/− SEM. P value was calculated using one way ANOVA followed by Sidak’s multiple comparison test