Fig. 3

Integration of gene expression and methylome data. a Scatterplot showing mean gene expression and boxplot showing mean DNA methylation in differentially methylated regions (DMRs) in treated group for DMRs in promoters (a) and DMRs in gene bodies (b), with lines representing a linear trend. Bars in the box plot correspond to the median. The lower and upper hinges correspond to the first and third quartiles (the 25th and 75th percentiles). The lower/upper whisker extends from the hinge to the smallest/largest value no further than 1.5 * IQR (inter quartile range) from the hinges. c–d Scatterplots displaying the effect of lipopolysaccharide (LPS) on the transcriptome and the methylome when compared to the control group; change in gene expression (log₂ Fold Change) is plotted against change in DNA methylation for c promoters of 12,115 genes and (d) gene bodies of 13,263 genes. Highlighted points denote genes with |ΔMethylation| > 5% and | Δexpression log₂FC| > 1; hypermethylated/increased expression (yellow), hypermethylated/lower expression (blue), hypomethylated/increased expression (green) and hypomethylated/lower expression (red)