EpigenPlot is a web tool for the efficient exploration of colorectal adenocarcinoma methylation data utilizing 2,346 tumor and normal samples.
Please cite kindly cite our paper to support further development: Muller, D., & Gyorffy, B. (2025). EpigenPlot: An interactive web platform for DNA methylation-based biomarker and drug target discovery in colorectal cancer., British Journal of Pharmacology (BJP), https://doi.org/10.1111/bph.17455
Copyright: Department of Bioinformatics, Semmelweis University 2021-2025
Check our other webtools: https://tnmplot.com ; http://www.kmplot.com ; http://www.rocplot.com ;
Choose a gene and a region and push the "Create plots" button in order to visualize methylation changes. The first plot includes a boxplot comparing β values of different tissue types, while the second one the difference between normal and adenocarcinoma values by percentiles.
Choose a gene to visualize all methylatable sites in a lollipop plot. Use the slide to narrow down the analyzed chromosome section. Use the cursor to select CpG-sites. Information of the selected site(s) will appear(s) in the table.
Choose a region and a KEGG pathway and push the "Create plots" button in order to visualize the difference between β value means of the genes associated with the selected KEGG pathway (human only). On the created comet plot, the end of the comet tail represents the mean of β values in normal, while the head represents the mean of β values in adenocarcinoma tissues. If there are more than 20 genes associated to the pathway, only the first N (default N = 20) with the most significant difference will be included in the plot. Difference in case of all genes will be shown in the table.
Gene regions and statistics
Gene region with significan differential methylation (p < 0.001, Kruskal-Wallis and β >= 0.2) with 5-fold cross-validates AUC and statistics. See the description of colum names in the first table tab.
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What kind of data is EpigenPlot based on?
EpigenPlot is a platform for user-friendly methylation data analysis. It facilitates the analysis of a curated dataset based on publicly available methylation data. The dataset includes data from two Illumina microarray platforms: IlluminaHumanMethylation450K (HM450K) and IlluminaHumanMethylationEPIC (EPIC).
What does beta value mean?
Methylation is shown in beta values representing a ratio of methylated and unmethylated signals. Beta values lie between 0 and 1 and are positively correlated with the extent of methylation.