Colonic gene expression in 2 cycles DSS colitis followed by an additional recovery period of 3 weeks.

<p>(A) Venn diagram of the differentially expressed probe sets of the top 50 most upregulated genes (fold change compared to controls) after additional recovery (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068876#pone.0068876.s005" target="_blank">Table S4</a>). These genes were compared with the 72 genes identified in chronic colitis. In total, 34 genes were uniquely upregulated in the recovery group. Only 16 genes were common with chronic colitis. Eleven out of these 16 genes were common with the 27 common upregulated genes in chronic colitis. (B) To isolate the impact of recovery on gene expression unrelated to the degree of chronicity, we identified all significantly upregulated genes after additional recovery compared to 2 cycles DSS colitis followed by immediate sacrifice. We started from all significantly upregulated genes after 2 cycles of DSS followed by additional recovery. Of these 376 genes, 255 were also upregulated after 2 cycles of DSS while 90 genes were uniquely upregulated after additional recovery (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068876#pone.0068876.s006" target="_blank">Table S5</a>), accounting for 65 unique genes. Among these 65 genes, 8 genes coded for keratins (<i>KRT 4, KRT5, KRT6, KRT13, KRT14, KRT16, KRT17, KRT84</i>). The biological functions of the 65 genes uniquely upregulated after recovery are summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068876#pone-0068876-t001" target="_blank">Table 1</a>. (C) Individual fold change expression of the 90 unique genes significantly upregulated (fold change compared to controls) in 2 cycles DSS colitis with additional recovery vs. 2 cycles DSS colitis. The abbreviations of the individual genes and gene probe IDs are explained in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068876#pone.0068876.s005" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068876#pone.0068876.s006" target="_blank">Table S5</a>.