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Fig. 2 | Journal of Inflammation

Fig. 2

From: Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis

Fig. 2

Transcriptomics results of colon biopsy samples. a Principal component (PC) analysis. The plot displays all samples in the reduced PC1–PC2 plane covering 31% + 15% = 46% of the total data variance. It allows us to examine the relationships between the various groups and treatments. Remarkably, PC1 captured the (pure) DSS effect (black arrow), while PC2 captured the (pure) exposure effects of anatabine and nicotine (blue and red arrows, respectively). b Volcano plots for individual gene differential expressions. The horizontal axis represents the log2 differential expression (“fold changes”), and the vertical axis represents its statistical significance as -log10 FDR. c Number of differentially expressed genes. For the selected pairwise comparisons, the bar plot displays the number of genes with positive or negative fold changes with corresponding statistically significant FDR ≤ 0.05. Note that the lower FDR values observed for the “Ana 5/20 DSS” comparisons do not necessarily prefigure a reduction of biological effects, because the statistics underlying the FDR/p values also depend on the gene expression variance within the experimental groups. d High-level heatmap of the statistically significant differentially expressed genes for the selected pairwise comparisons. In order to provide a comprehensible display of the large (9728 × 5) fold-change matrix, we first normalized its rows to their maximum absolute values and then reordered them by hierarchical clustering (complete linkage method) on the basis of their Euclidean distances. e Scatter plot from the comparisons between the pure and exposure-modified DSS effects by using the differential gene expression results. The horizontal axis of the scatter plots represents the fold changes of the pure DSS effect (“Water DSS vs Water” pairwise comparison), whereas the vertical axis contains the corresponding values in case of anatabine or nicotine exposure (“anatabine/nicotine 5/20 DSS vs Water” pairwise comparisons). In an ideal case (included as a reference [first plot], the best-fitted straight line coincides with the diagonal (indicated in green), and its slope is equal to 1. The transcriptomics effects of anatabine or nicotine exposure were quantified by the slope of the best-fitted straight lines indicated on each plot. Nic 5, nicotine 5 mg/kg; Nic 20, nicotine 20 mg/kg; Ana 5, anatabine 5 mg/kg; Ana 20, anatabine 20 mg/kg

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