PiiL: visualization of DNA methylation and gene expression data in gene pathways

Area of Science:

• Epigenetics
• Genomics
• Bioinformatics

Background:

• DNA methylation is a key epigenetic mechanism regulating gene expression.
• Millions of CpG sites in vertebrate genomes offer potential methylation targets, but their specific effects are largely uncharacterized.
• Understanding the interplay between methylation, cellular programs, and phenotypes is crucial.

Purpose of the Study:

• To develop an interactive tool, PiiL, for analyzing the relationship between DNA methylation and gene expression.
• To facilitate hypothesis testing and pattern searching within gene pathways and regulatory networks.
• To investigate methylation and expression patterns in brain tumors.

Main Methods:

• Developed PiiL, an interactive gene expression pathway browser integrating methylation and expression data.
• Utilized data projected onto pathways from the KEGG database for analysis.
• Applied filtering methods to identify consistent CpG methylation patterns and their impact on gene expression.

Main Results:

• Confirmed that IDH gene mutations, not histology, predominantly separate methylation and expression patterns in brain tumors.
• Successfully inferred IDH mutation status for unknown samples.
• Identified specific CpG sites affecting key regulator gene expression and downstream genes in pathways.

Conclusions:

• PiiL provides a user-friendly platform for integrated analysis of DNA methylation and gene expression.
• The tool aids in understanding epigenetic regulation in complex diseases like brain tumors.
• PiiL is implemented in Java with source code available under GPL license.