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A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
Qiang Song1, Benjamin Decato, Elizabeth E Hong
1Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
Plos One
|December 11, 2013
Summary
Researchers can now analyze and compare DNA methylation patterns across eukaryotes with MethPipe and MethBase. These tools simplify the study of methylomes, aiding in understanding genomic phenomena and diseases.
Area of Science:
- Genomics
- Epigenetics
Background:
- DNA methylation plays a crucial role in eukaryotic gene regulation, evolution, and disease.
- Whole-genome bisulfite sequencing (WGBS) provides single-base resolution for DNA methylation analysis.
- The increasing volume of public WGBS data necessitates efficient analysis and comparison tools.
Purpose of the Study:
- To introduce MethPipe, a comprehensive bioinformatics pipeline for methylome analysis.
- To present MethBase, a database of publicly available, annotated methylomes.
- To facilitate the comparison and feature extraction from diverse methylome datasets.
Main Methods:
- Development of MethPipe for both low and high-level methylome analysis.
- Compilation and annotation of public methylome data into the MethBase database.
- Utilizing WGBS data for single-base resolution methylation studies.
Main Results:
- MethPipe offers robust tools for processing and analyzing methylome data.
- MethBase provides a centralized resource for accessing and comparing annotated methylomes.
- The combined resources enable effective extraction and comparison of genomic methylation features.
Conclusions:
- MethPipe and MethBase significantly enhance the ability to study DNA methylation patterns.
- These tools are vital for researchers investigating genomic phenomena, evolutionary processes, and diseases.
- Facilitates comparative methylomics research using public data.
