Analysing and interpreting DNA methylation data - PubMed (original) (raw)

Review

. 2012 Oct;13(10):705-19.

doi: 10.1038/nrg3273.

Affiliations

• PMID: 22986265
• DOI: 10.1038/nrg3273

Review

Analysing and interpreting DNA methylation data

Christoph Bock. Nat Rev Genet. 2012 Oct.

Abstract

DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range of biological processes and diseases. The technology is now available for studying DNA methylation genome-wide, at a high resolution and in a large number of samples. This Review discusses relevant concepts, computational methods and software tools for analysing and interpreting DNA methylation data. It focuses not only on the bioinformatic challenges of large epigenome-mapping projects and epigenome-wide association studies but also highlights software tools that make genome-wide DNA methylation mapping more accessible for laboratories with limited bioinformatics experience.

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References

1. 1. Brief Bioinform. 2008 May;9(3):189-97 - PubMed
2. 1. Cell. 2011 Feb 4;144(3):439-52 - PubMed
3. 1. Epigenomics. 2011 Dec;3(6):771-84 - PubMed
4. 1. Nucleic Acids Res. 2008 Jun;36(10):e55 - PubMed
5. 1. J Clin Oncol. 2011 Mar 20;29(9):1133-9 - PubMed

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