Title |
A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome
|
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Published in |
BMC Genomics, November 2012
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DOI | 10.1186/1471-2164-13-630 |
Pubmed ID | |
Authors |
Daniel Capurso, Hao Xiong, Mark R Segal |
Abstract |
Applying supervised learning/classification techniques to epigenomic data may reveal properties that differentiate histone modifications. Previous analyses sought to classify nucleosomes containing histone H2A/H4 arginine 3 symmetric dimethylation (H2A/H4R3me2s) or H2A.Z using human CD4+ T-cell chromatin immunoprecipitation sequencing (ChIP-Seq) data. However, these efforts only achieved modest accuracy with limited biological interpretation. Here, we investigate the impact of using appropriate data pre-processing -deduplication, normalization, and position- (peak-) finding to identify stable nucleosome positions - in conjunction with advanced classification algorithms, notably discriminatory motif feature selection and random forests. Performance assessments are based on accuracy and interpretative yield. |
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