Fig. 5: Intersection analysis of DNAm-linked DEGs in vivo and in vitro models.

a Gene ontology analysis for biological processes enriched in DEGs in Dnmt3a^ΔIEC and Dnmt3a^fl/fl mice. Dot size is proportional to the gene ratio and color corresponds to the p-value of enrichment (two-sided). Top selected GO terms are shown. b Comparison of transcription-methylation correlation between in vitro and in vivo models. Blue and green dots represent the rescued genes that are correlated with one or more nearby DMPs in vitro and in vivo, respectively. Brown dots represent the rescued genes that are correlated with one or more nearby DMPs in both models. c Common genes regulated by DNMT3A in Caco-2 model (in vitro) and in mouse model (in vivo). Gene expression (left panels) (n = 4) and DNA methylation levels (right panels) (n = 4) of RGS14 (Rgs14), IFITM3 (Ifitm3), and COX6B1 (Cox6b1) are shown. Within each boxplot, the horizontal lines denote the median values and the boxes extend from the 25th to the 75th quartile of the distribution. The vertical lines extend to the most extreme values within 1.5 interquartile range of the 25th and 75th percentile of the distribution. P-values are calculated using the DESeq2 method for the transcriptomic data and the hierarchical linear model (limma) for the methylation data. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.