| Registro completo |
| Provedor de dados: |
ArchiMer
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| País: |
France
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| Título: |
Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
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| Autores: |
Bulla, Ingo
Aliaga, Benoit
Lacal, Virginia
Bulla, Jan
Grunau, Christoph
Chaparro, Cristian
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| Data: |
2018
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| Ano: |
2018
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| Palavras-chave: |
Epigenetics
DNA methylation
Kernel density estimation
CpG o/e ratio
CpN o/e ratio
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| Resumo: |
Background: DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. Results: Predominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions without a priori assumptions about the underlying distributions. Conclusions: We show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.
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| Tipo: |
Text
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| Idioma: |
Inglês
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| Identificador: |
https://archimer.ifremer.fr/doc/00437/54816/71790.pdf
https://archimer.ifremer.fr/doc/00437/54816/71791.pdf
https://archimer.ifremer.fr/doc/00437/54816/71792.csv
https://archimer.ifremer.fr/doc/00437/54816/71793.pdf
https://archimer.ifremer.fr/doc/00437/54816/72014.pdf
https://archimer.ifremer.fr/doc/00437/54816/72015.csv
https://archimer.ifremer.fr/doc/00437/54816/72016.csv
DOI:10.1186/s12859-018-2115-4
https://archimer.ifremer.fr/doc/00437/54816/
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| Editor: |
Biomed Central Ltd
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| Formato: |
application/pdf
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| Fonte: |
Bmc Bioinformatics (1471-2105) (Biomed Central Ltd), 2018 , Vol. 19 , N. 105 , P. 13p.
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| Direitos: |
info:eu-repo/semantics/openAccess
restricted use
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