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. 2018 Feb;154(3):585–598. doi: 10.1053/j.gastro.2017.10.007

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© 2018 The AGA Institute All rights reserved.

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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Differential DNAm and gene expression analysis were performed separately for terminal ileum (TI) (A and B) and sigmoid colon (SC) (C and D), taking mucosal inflammation into account. (A and C) Venn diagrams of significant differentially methylated positions (DMPs), differentially expressed genes (DEGs), and regulatory DMRs (rDMRs). (B and D) Example of disease-specific rDMRs displaying DNA methylation levels expressed as Beta value on the y-axis in the left panel separately for TI and SC samples in the upper and lower panel, respectively. Beta value of 0 represents un-methylated, while 1 represents fully methylated CpG site. Genomic location is indicated on the x-axis. The middle panel displays identified rDMR (enlarged). The right panel displays a boxplot of the respective gene expression according to diagnosis. (B) rDMR within the APOA1 identified in TI-derived epithelium of children diagnosed with CD. (D) rDMR within the BACH2 gene identified in colonic IEC.