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Fig. 2 | Clinical Epigenetics

Fig. 2

From: A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples

Fig. 2

Identification of differential methylation. a Boxplot of global cfDNA methylation in NCF, AN, AA, and CRC pools. Global methylation is expressed as the average methylation rate for each pooled sample. The box plot represents the median (line across the box), interquartile range, and maximum and minimum values (whiskers). b Manhattan plot showing −log10(p value) resulting from the differential methylation analysis for all the CpGs considered (703,653). The p values are sorted by chromosome coordinates. Significant DMPs between AN and NCF pooled samples with a FDR < 5% (5808) appear highlighted in darker color, above the red dashed line. c Volcano plot of differential methylation −log10(p value) versus differences in methylation levels (Δbeta: obtained by subtracting the DNA methylation levels (beta values) of NCF from AN). Significant DMPs appear above the red dashed line (FDR 5%). Significant DMPs with a difference in the methylation levels greater than 10% (1384) are highlighted in color (135 hypermethylated DMPs in AN, orange dots: Δbeta > 0.1 and FDR < 5%; 1249 hypomethylated DMPs in AN, blue dots: Δbeta < − 0.1 and FDR < 5%). d Relative distribution of the 1385 DMPs with absolute Δbeta > 0.1 in relation to CpG islands (CGI) and across different genomic regions. The EPIC array categorizes probes following a functional classification into three major groups: promoter regions (5′UTR, TSS200, TSS1500, and first exons), intragenic regions (gene body and 3′UTR), and intergenic regions. TSS200, TSS1500: 200 and 1500 bp upstream the transcription start site, respectively. CGI-shore: sequences 2 kb flanking the CGI, CGI-shelf: sequences 2 kb flanking shore regions, opensea: sequences located outside these regions [30]

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