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We are analyzing https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-215.

Title:
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments | BMC Bioinformatics | Full Text
Description:
Background Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies have demonstrated the value of this precision: meaningful features that correlate strongly with biological functions can be found associated with only a few CpG sites. Understanding the role of DNA methylation, and more broadly the role of DNA accessibility, requires that methylation differences between populations of cells are identified with extreme precision and in complex experimental designs. Results In this work we investigated the use of beta-binomial regression as a general approach for modeling whole-genome bisulfite data to identify differentially methylated sites and genomic intervals. Conclusions The regression-based analysis can handle medium- and large-scale experiments where it becomes critical to accurately model variation in methylation levels between replicates and account for influence of various experimental factors like cell types or batch effects.
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25 years and 10 months (reg. 1999-08-06).

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Keywords {🔍}

methylation, regions, samples, article, methylated, pubmed, google, scholar, cpgs, betabinomial, differentially, levels, method, analysis, regression, distribution, cas, sites, dna, methods, detection, site, coverage, differential, test, parameter, beta, central, data, replicates, wgbs, variation, level, individual, based, additional, file, cpg, model, authors, bmc, bisulfite, sequencing, sample, set, datasets, pvalues, dataset, figure, experiments,

Topics {✒️}

genome-wide high-resolution mapping log-odds ratio 𝜋 𝑖 log-likelihood ratio test 𝑗 𝜂 𝑗 𝑧 𝑗 log-odds-ratios 𝑝 ̂ 𝑖 epigenome-wide association studies bmc bioinformatics 15 fdr corrected p-values extra-binomial variation increases genome-wide prior distribution authors scientific editing privacy choices/manage cookies central neuroendocrine cells beta-binomial distribution retains optimally weighted z-test frontal cortex samples single nucleotide resolution source code released nucleotide-resolution view genome bisulfite sequencing genome-wide scale dm-detection method based complex experimental designs article dolzhenko beta-binomial dispersion parameter genome-wide prior bisulfite sequencing data large-scale experiments global epigenomic reconfiguration complicated methylation profiles human dna methylomes genome bisulfite data typically involve methylomes 152 methylc-seq libraries neurone-specific enolase adult hematopoietic compartment population epigenomic diversity intermediate methylation levels authors’ original file detect differential methylation link function sequencing-based studies full size image assessing differential methylation exhibit differential methylation bmc common human diseases

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