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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| Published in | Genome research Vol. 26; no. 2; pp. 256 - 262 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Cold Spring Harbor Laboratory Press
01.02.2016
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1088-9051 1549-5469 1549-5469 |
| DOI | 10.1101/gr.196394.115 |
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| Abstract | 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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| AbstractList | 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.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. 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. |
| Author | Jühling, Frank Kretzmer, Helene Stadler, Peter F. Hoffmann, Steve Bernhart, Stephan H. Otto, Christian |
| AuthorAffiliation | 1 Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany 2 Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany 5 Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria 4 Santa Fe Institute, Santa Fe, New Mexico 87501, USA 6 Max Planck Institute for Mathematics in Sciences, 04103 Leipzig, Germany 3 RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology - IZI, 04103 Leipzig, Germany |
| AuthorAffiliation_xml | – name: 1 Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany – name: 2 Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany – name: 3 RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology - IZI, 04103 Leipzig, Germany – name: 5 Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria – name: 6 Max Planck Institute for Mathematics in Sciences, 04103 Leipzig, Germany – name: 4 Santa Fe Institute, Santa Fe, New Mexico 87501, USA |
| Author_xml | – sequence: 1 givenname: Frank surname: Jühling fullname: Jühling, Frank – sequence: 2 givenname: Helene surname: Kretzmer fullname: Kretzmer, Helene – sequence: 3 givenname: Stephan H. surname: Bernhart fullname: Bernhart, Stephan H. – sequence: 4 givenname: Christian surname: Otto fullname: Otto, Christian – sequence: 5 givenname: Peter F. surname: Stadler fullname: Stadler, Peter F. – sequence: 6 givenname: Steve surname: Hoffmann fullname: Hoffmann, Steve |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26631489$$D View this record in MEDLINE/PubMed https://hal.science/hal-02517265$$DView record in HAL |
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| ContentType | Journal Article |
| Copyright | 2016 Jühling et al.; Published by Cold Spring Harbor Laboratory Press. Distributed under a Creative Commons Attribution 4.0 International License 2016 |
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| License | 2016 Jühling et al.; Published by Cold Spring Harbor Laboratory Press. Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0 This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
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| Snippet | The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel... |
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| SubjectTerms | 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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