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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Methylation plotter: a web tool for dynamic visualization of DNA methylation data.

Izaskun Mallona¹, Anna Díez-Villanueva¹, Miguel A Peinado¹

¹Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Ctra. de Can Ruti, camí de les escoles, s/n, 08916 Badalona, Spain ; Health Research Institute Germans Trias i Pujol (IGTP), Ctra. de Can Ruti, camí de les escoles, s/n, 08916 Badalona, Spain.

Source Code for Biology and Medicine

|September 27, 2014

Summary

This summary is machine-generated.

Methylation plotter is a user-friendly web tool for visualizing DNA methylation data, offering publication-ready graphics and statistical analysis for genomic regions. It aids researchers in understanding methylation patterns across samples and groups.

Keywords:

Lollipop plot Methylation plot Methylation visualization R/shiny

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Area of Science:

Bioinformatics
Genomics
Epigenetics

Background:

DNA methylation is a crucial epigenetic mechanism influencing gene expression.
Visualizing and analyzing large-scale methylation data is essential for biological research.
Existing tools may lack user-friendliness or comprehensive visualization options.

Purpose of the Study:

To develop and present Methylation plotter, a web-based tool for intuitive visualization of DNA methylation data.
To provide publication-ready graphical representations of methylation status for genomic regions.
To offer integrated statistical analysis for methylation data.

Main Methods:

The tool utilizes R/Shiny for a dynamic user interface.
Users upload methylation status data for genomic regions (up to 100 samples, 100 CpGs).
Supports sample grouping (e.g., tumor vs. normal) and various data arrangement options.

Main Results:

Generates interactive lollipop or grid plots summarizing CpG methylation status across samples.
Produces methylation profile plots, boxplots for group comparisons, and dendrograms for clustering.
Includes descriptive statistics and statistical testing for CpG and group level differences.

Conclusions:

Methylation plotter provides a powerful, accessible platform for DNA methylation data visualization and analysis.
The tool simplifies the process of generating high-quality figures for scientific publications.
It facilitates deeper insights into epigenetic patterns and their biological implications.