2018
DOI: 10.1101/261982
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Example of Methylome Analysis with MethylIT using Cancer Datasets

Abstract: Methyl-IT, a novel methylome analysis procedure based on information thermodynamics and signal detection was recently released. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Methyl-IT enhances the resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods. Herein, an… Show more

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“…Putative promoter regions were classed as 500bp upstream of each gene's 5' UTR and intergenic regions were all other unannotated regions, although we acknowledge these regions likely include transposable elements. The extent of variability in DNA methylation levels across developmental stages was assessed using the Jensen-Shannon divergence (JSD) index implemented by the MethylIT 0.3.2.3 R package (Sanchez, 2021). Genes were classed as showing significant variability across developmental states when the JSD index was >0.037 based on the distribution of all indices (supplementary Fig.…”
Section: Dna Methylation DI Erences Between Developmental Stagesmentioning
confidence: 99%
“…Putative promoter regions were classed as 500bp upstream of each gene's 5' UTR and intergenic regions were all other unannotated regions, although we acknowledge these regions likely include transposable elements. The extent of variability in DNA methylation levels across developmental stages was assessed using the Jensen-Shannon divergence (JSD) index implemented by the MethylIT 0.3.2.3 R package (Sanchez, 2021). Genes were classed as showing significant variability across developmental states when the JSD index was >0.037 based on the distribution of all indices (supplementary Fig.…”
Section: Dna Methylation DI Erences Between Developmental Stagesmentioning
confidence: 99%