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DMRFusion: A differentially methylated region detection tool based on the ranked fusion method |
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| Authors: | Maryam Yassi Ehsan Shams Davodly Afsaneh Mojtabanezhad Shariatpanahi Mehdi Heidari Mahdieh Dayyani Alireza Heravi-Moussavi Mohammad Hossein Moattar Mohammad Amin Kerachian |
| Institution: | 1. Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran;2. Canada''s Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, British Columbia, Canada;3. Department of Computer Engineering, Mashhad Branch, Islamic Azad University, Mashhad, Iran;4. Cancer Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran;5. Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran |
| Abstract: | 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 < 0.05 and type I error: 0.04). |
| Keywords: | DNA methylation Epigenetic Differentially methylated regions Reduced representation bisulfite sequencing Filter method |
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