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Literature DB >> 22986265

Analysing and interpreting DNA methylation data.

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.

Mesh：

Year: 2012 PMID： 22986265 DOI： 10.1038/nrg3273

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 53.242

156 in total

Review 1. Phenotypic plasticity and the epigenetics of human disease.

Authors: Andrew P Feinberg
Journal: Nature Date: 2007-05-24 Impact factor: 49.962

2. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Authors: Elena Y Harris; Nadia Ponts; Karine G Le Roch; Stefano Lonardi
Journal: Bioinformatics Date: 2012-05-03 Impact factor: 6.937

3. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.

Authors: Reid F Thompson; Masako Suzuki; Kevin W Lau; John M Greally
Journal: Bioinformatics Date: 2009-06-26 Impact factor: 6.937

4. MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.

Authors: Mattia Pelizzola; Yasuo Koga; Alexander Eckehart Urban; Michael Krauthammer; Sherman Weissman; Ruth Halaban; Annette M Molinaro
Journal: Genome Res Date: 2008-09-02 Impact factor: 9.043

5. Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists.

Authors: Michael Hackenberg; Rune Matthiesen
Journal: Bioinformatics Date: 2008-04-23 Impact factor: 6.937

6. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.

Authors: B H Ramsahoye; D Biniszkiewicz; F Lyko; V Clark; A P Bird; R Jaenisch
Journal: Proc Natl Acad Sci U S A Date: 2000-05-09 Impact factor: 11.205

7. Increased methylation variation in epigenetic domains across cancer types.

Authors: Kasper Daniel Hansen; Winston Timp; Héctor Corrada Bravo; Sarven Sabunciyan; Benjamin Langmead; Oliver G McDonald; Bo Wen; Hao Wu; Yun Liu; Dinh Diep; Eirikur Briem; Kun Zhang; Rafael A Irizarry; Andrew P Feinberg
Journal: Nat Genet Date: 2011-06-26 Impact factor: 38.330

8. The Genomic HyperBrowser: inferential genomics at the sequence level.

Authors: Geir K Sandve; Sveinung Gundersen; Halfdan Rydbeck; Ingrid K Glad; Lars Holden; Marit Holden; Knut Liestøl; Trevor Clancy; Egil Ferkingstad; Morten Johansen; Vegard Nygaard; Eivind Tøstesen; Arnoldo Frigessi; Eivind Hovig
Journal: Genome Biol Date: 2010-12-23 Impact factor: 13.583

9. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

Authors: Eun-Joon Lee; Lirong Pei; Gyan Srivastava; Trupti Joshi; Garima Kushwaha; Jeong-Hyeon Choi; Keith D Robertson; Xinguo Wang; John K Colbourne; Lu Zhang; Gary P Schroth; Dong Xu; Kun Zhang; Huidong Shi
Journal: Nucleic Acids Res Date: 2011-07-23 Impact factor: 16.971

10. Visualization of genomic data with the Hilbert curve.

Authors: Simon Anders
Journal: Bioinformatics Date: 2009-03-17 Impact factor: 6.937

234 in total

Review 1. A Molecular Perspective on Procedures and Outcomes with Assisted Reproductive Technologies.

Authors: Monica A Mainigi; Carmen Sapienza; Samantha Butts; Christos Coutifaris
Journal: Cold Spring Harb Perspect Med Date: 2016-04-01 Impact factor: 6.915

Review 2. Advances in the profiling of DNA modifications: cytosine methylation and beyond.

Authors: Nongluk Plongthongkum; Dinh H Diep; Kun Zhang
Journal: Nat Rev Genet Date: 2014-08-27 Impact factor: 53.242

3. ChAMP: 450k Chip Analysis Methylation Pipeline.

Authors: Tiffany J Morris; Lee M Butcher; Andrew Feber; Andrew E Teschendorff; Ankur R Chakravarthy; Tomasz K Wojdacz; Stephan Beck
Journal: Bioinformatics Date: 2013-12-12 Impact factor: 6.937

Review 4. From promises to practical strategies in epigenetic epidemiology.

Authors: Jonathan Mill; Bastiaan T Heijmans
Journal: Nat Rev Genet Date: 2013-07-02 Impact factor: 53.242

Review 5. Towards incorporating epigenetic mechanisms into carcinogen identification and evaluation.

Authors: Zdenko Herceg; Marie-Pierre Lambert; Karin van Veldhoven; Christiana Demetriou; Paolo Vineis; Martyn T Smith; Kurt Straif; Christopher P Wild
Journal: Carcinogenesis Date: 2013-06-07 Impact factor: 4.944

Review 6. Recommendations for the design and analysis of epigenome-wide association studies.

Authors: Karin B Michels; Alexandra M Binder; Sarah Dedeurwaerder; Charles B Epstein; John M Greally; Ivo Gut; E Andres Houseman; Benedetta Izzi; Karl T Kelsey; Alexander Meissner; Aleksandar Milosavljevic; Kimberly D Siegmund; Christoph Bock; Rafael A Irizarry
Journal: Nat Methods Date: 2013-10 Impact factor: 28.547