PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data
| العنوان: | PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data |
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| المؤلفون: | James S. Blachly, Mike W. Zoller, Pearlly S. Yan, Ralf Bundschuh, Mark Murphy, Javkhlan-Ochir Ganbat, John C. Byrd, Jincheol Park, Shili Lin, David Frankhouser, John Curfman, Guido Marcucci |
| المصدر: | Bioinformatics. 30:3567-3574 |
| بيانات النشر: | Oxford University Press (OUP), 2014. |
| سنة النشر: | 2014 |
| مصطلحات موضوعية: | Statistics and Probability, Bisulfite sequencing, Genomics, Biology, Biochemistry, Humans, Sulfites, Methylated DNA immunoprecipitation, Molecular Biology, Genetics, Nucleotides, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Methylation, DNA Methylation, Gene signature, Original Papers, Computer Science Applications, Leukemia, Myeloid, Acute, Computational Mathematics, Computational Theory and Mathematics, CpG site, DNA methylation, Illumina Methylation Assay, CpG Islands, Algorithms |
| الوصف: | Motivation : DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques. Results : Here we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing and has better predictive power with respect to a reference than window-based methods, often used for enrichment data. The described method was used to produce the methylation data used in tandem with gene expression to produce a novel and clinically significant gene signature in acute myeloid leukemia. In addition, we introduce a complementary statistical method that uses this nucleotide-resolution methylation data for detection of differentially methylated features. Availability : Software in the form of Python and R scripts is available at http://bioserv.mps.ohio-state.eduTest/ premer and is free for non-commercial use. Contact : pearlly.yan@osumc.edu ; bundschuh@mps.ohio-state.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
| تدمد: | 1367-4811 1367-4803 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee9364ee17b2ca106fc4acbe839a76feTest https://doi.org/10.1093/bioinformatics/btu583Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....ee9364ee17b2ca106fc4acbe839a76fe |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13674811 13674803 |
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