Journal
GENOME RESEARCH
Volume 26, Issue 2, Pages 256-262Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.196394.115
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Funding
- German Bundesministerium fur Bildung und Forschung (BMBF)
- German Bundesministerium fur Bildung und Forschung (PTJ grant) [HNPCCSys 031 6065A]
- German Bundesministerium fur Bildung und Forschung (ICGC MMML-Seq) [01KU1002J]
- European Union [HEALTH-F5-2011-282510]
- LIFE: Leipzig Research Center for Civilization Diseases, University of Leipzig
- European Union
- European Regional Development Fund (ERDF)
- European Social Fund (ESF)
- Free State of Saxony within the framework of the excellence initiative
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The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results.
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