Data/hora: 11/06/2024 04:07:40

Provedor de dados: | Institutional Archive of Ifreme (ArchiMer)
País: | France
Título: | Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
Autores: | Bulla, Ingo; Aliaga, Benoit; Lacal, Virginia; Bulla, Jan; Grunau, Christoph; Chaparro, Cristian.
Data: | 2018
Ano: | 2018
Palavras-chave: | Epigenetics; DNA methylation; Kernel density estimation; CpG o/e ratio; CpN o/e ratio.
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.
Tipo: | Text
Idioma: | Inglês

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/

Editor: | Biomed Central Ltd
Formato: | application/pdf
Fonte: | Bmc Bioinformatics (1471-2105) (Biomed Central Ltd), 2018 , Vol. 19 , N. 105 , P. 13p.

Fonte:

info:eu-repo/semantics/openAccess

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