Figure 7.

Exposure to the TWD prior to, during and after DSS-induced gut injury intensified changes in expression of genes associated with immune and cancer pathways as compared to mice fed AIN (Experiment E). (A) Principal components analyses (PCA) of differentially expressed genes (BH q < 0.05, log₂ ratio > 1 or < −1) in colon tissues of mice fed either AIN or TWD prior to DSS (Pre-DSS), during active colitis (Colitis), or two weeks later during recovery (Recovery). PC1 and PC2 are shown with the 95% prediction ellipse. Because only three genes met all significance criteria at the Pre-DSS time point, all genes differently expressed by at least two-fold with an FDR p < 0.10 were used for the PCA analysis for that time point only. (B) Unsupervised, bidirectional hierarchical cluster analysis of colon transcriptome data using the Euclidean distance method with average linkage. For each time point, the heatmap shows all genes differentially expressed between TWD and AIN diet groups colored by the log₂ ratio calculated with respect to AIN/Pre-DSS. (C) Bar charts indicate the number of genes differentially expressed at each time point for selected immune and cancer pathways. The total number of genes affiliated with each pathway for the PanCancer Immune panel are indicated in parentheses.