Algorithms for CpG Islands Search: New Advantages and Old Problems

Medvedeva, Yulia A.

doi:10.5772/22883

Cited by 3 publications

(1 citation statement)

References 134 publications

(146 reference statements)

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“…It has several features, the most important of which include setting the desired percentage of GC dinucleotides and the desired the size of CpG islands. The main advantage of the program is that there is no restriction on the amount of input sequence data [7]. The algorithm CpG Island Searcher® used stringent criteria (usually referred to as Takai-Jones algorithm [8]): length ≥ 500 bp, GC content ≥ 55%, and ObsCpG/ExpCpG ≥ 0.65 [9].…”

Section: A Review Of Epigenetic Programsmentioning

confidence: 99%

In silico analysis of methylation of the selected genes using computer programs based on various analytical techniques

Gryzińska

Jakubczak

Stryjecki

et al. 2015

Biocybernetics and Biomedical Engineering

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Section: A Review Of Epigenetic Programsmentioning

confidence: 99%

In silico analysis of methylation of the selected genes using computer programs based on various analytical techniques

Gryzińska

Jakubczak

Stryjecki

et al. 2015

Biocybernetics and Biomedical Engineering

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Experimental Design and Bioinformatic Analysis of DNA Methylation Data

Medvedeva

Shershebnev

2018

Methods in Molecular Biology

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DNA methylation is a crucial regulatory mechanism of gene expression, affected in many human pathologies. Therefore, it is not surprising that nowadays, in the era of high-throughput methods, a lot of data sets representing DNA methylation in various conditions are available and the amount of such data keeps growing. In this chapter, we discuss those aspects of experiment planning and data analysis, which we consider the most important for reliability and reproducibility of DNA methylation studies: usage of replicates, data quality control at various stages, selection of a statistical model, and incorporation of DNA methylation into the multi-omics analysis.

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CpG traffic lights are markers of regulatory regions in humans

Khamis

et al. 2016

Preprint

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DNA methylation is involved in regulation of gene expression. Although modern methods profile DNA methylation at single CpG sites, methylation levels are usually averaged over genomic regions in the downstream analyses. In this study we demonstrate that single CpG methylation can serve as a more accurate predictor of gene expression compared to average promoter / gene body methylation. CpG positions with significant correlation between methylation and expression of a gene nearby (named CpG traffic lights) are evolutionary conserved and enriched for exact TSS positions and active enhancers. Among all promoter types, CpG traffic lights are especially enriched in poised promoters. Genes that harbor CpG traffic lights are associated with development and signal transduction. Methylation levels of individual CpG traffic lights vary between cell types dramatically with the increased frequency of intermediate methylation levels, indicating cell population heterogeneity in CpG methylation levels. Being in line with the concept of the inherited stochastic epigenetic variation, methylation of such CpG positions might contribute to transcriptional regulation. Alternatively, one can hypothesize that traffic lights are markers of absent gene expression resulting from inactivation of their regulatory elements. The CpG traffic lights provide a promising insight into mechanisms of enhancer activity and gene regulation linking methylation of single CpG to expression.

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Algorithms for CpG Islands Search: New Advantages and Old Problems

Cited by 3 publications

References 134 publications

In silico analysis of methylation of the selected genes using computer programs based on various analytical techniques

In silico analysis of methylation of the selected genes using computer programs based on various analytical techniques

Experimental Design and Bioinformatic Analysis of DNA Methylation Data

CpG traffic lights are markers of regulatory regions in humans

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