Fig. 4: Differences in host DNA methylation and gene expression across subject groups with regards to inflammation and microbiota clustering. | Nature Communications

Fig. 4: Differences in host DNA methylation and gene expression across subject groups with regards to inflammation and microbiota clustering.

From: Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

Fig. 4

Significant differential host DNA methylation [beta values; significance determined using mixed linear models from lme4 library, adjusted with FDR] with corresponding gene expression [log2(fragments per kilobase of transcript per million mapped reads)] of examples of immune-related genes in a inflamed/non-inflamed CD tissue, b microbiota clusters 1–3 (expression, using stattest from the ballgown library, was significant before adjustment for multiple testing with FDR, and for a subset of 71 matching samples; extreme outliers removed to improve clarity; gene body methylation in NOTCH4, DRAM1, and TRIM27 (b), promoter methylation in SELE (a) and CCDC88B (b)) (box plot lower and upper sides show 25th and 75th percentiles, respectively. The whiskers are 1.5 of the interquartile range). c Epigenome principal component analysis outlining the inflammation- (PC1) and disease- (PC6) associated epigenetic trends.

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