Figure 4.

Identification of genes with coordinated changes in DNA methylation and gene expression. (a) Quadrant plot of DMRs and expression of associated genes. On the x axis is the −log₁₀ Fisher’s P value (see Online Methods) for differentially methylated regions; on the y axis, −log₁₀ P value of differential expression for associated genes. Vertical dashed lines indicate a threshold of 5% FDR and horizontal dashed lines indicate a threshold corresponding to P < 0.05. The four quadrants shown are (i) hypermethylated and upregulated in multiple sclerosis (open green circles), (ii) hypermethylated and downregulated in multiple sclerosis (filled green circles), (iii) hypomethylated and upregulated in multiple sclerosis (filled red circles) and (iv) hypomethylated and downregulated in multiple sclerosis (open red circles). A select number of genes are shown as position references. (b) Box-and-whisker plot of normalized log₂ expression for several upregulated and downregulated genes associated with a DMR. Whiskers indicate 1.5 times the interquartile range; bottom and top of the boxes, first and third quartiles, respectively; center lines, second quartile. Open circles represent measurements outside of the range defined by the whiskers. MS, multiple sclerosis.