metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
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 algorit...
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| Veröffentlicht in: | Genome research 2016-02, Vol.26 (2), p.256-262 |
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| creator | Jühling, Frank Kretzmer, Helene Bernhart, Stephan H Otto, Christian Stadler, Peter F Hoffmann, Steve |
| description | 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. |
| doi_str_mv | 10.1101/gr.196394.115 |
| format | Article |
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| subjects | Algorithms Biochemistry, Molecular Biology Case-Control Studies Cerebellar Neoplasms - genetics CpG Islands DNA Methylation Genomics Humans Life Sciences Medulloblastoma - genetics Method Quantitative Methods Sequence Analysis, DNA Software |
| title | metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data |
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