DMRFusion: A differentially methylated region detection tool based on the ranked fusion method

DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylatio...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2018-11, Vol.110 (6), p.366-374
Main Authors: Yassi, Maryam, Shams Davodly, Ehsan, Mojtabanezhad Shariatpanahi, Afsaneh, Heidari, Mehdi, Dayyani, Mahdieh, Heravi-Moussavi, Alireza, Moattar, Mohammad Hossein, Kerachian, Mohammad Amin
Format: Article
Language:English
Subjects:
Differentially methylated regions
DNA Methylation
Epigenetic
Epigenomics - methods
Filter method
Humans
Leukemia, Prolymphocytic, T-Cell - genetics
Leukemia, Prolymphocytic, T-Cell - metabolism
Reduced representation bisulfite sequencing
Sequence Analysis, DNA - methods
Software
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Summary:DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test. In this study, DMRFusion on reduced representation bisulfite sequencing (RRBS) data in chronic lymphocytic leukemia cancer displayed 30 nominated regions and CpG sites with a maximum methylation difference detected in the hypermethylation DMRs. We realized that DMRFusion is able to process methylation sequencing data in an efficient and accurate manner and to provide annotation and visualization for DMRs with high fold difference score (p-value and FDR
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2017.12.006