Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data
نویسندگان
چکیده
منابع مشابه
Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data
Motivation DNA methylation is an important epigenetic mechanism in gene regulation and the detection of differentially methylated regions (DMRs) is enthralling for many disease studies. There are several aspects that we can improve over existing DMR detection methods: (i) methylation statuses of nearby CpG sites are highly correlated, but this fact has seldom been modelled rigorously due to the...
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Whole genome bisulfite sequencing (WGBS) is the current method of choice to obtain the methylation status of each single CpG dinucleotide in a genome. The typical analysis asks for regions that are differentially methylated (DMRs) between samples of two classes, such as different cell types. However, even with current low sequencing costs, many studies need to cope with few samples and medium c...
متن کاملDetection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Recent developments in whole genome bisulfite sequencing (WGBS) technology have enabled genome-wide measurements of DNA methylation at single base pair resolution. Many experiments have been conducted to compare DNA methylation profiles under different biological contexts, with the goal o...
متن کاملDetection of significantly differentially methylated regions in targeted bisulfite sequencing data
MOTIVATION Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer an...
متن کاملIdentification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing
We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capt...
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ژورنال
عنوان ژورنال: Methods
سال: 2021
ISSN: 1046-2023
DOI: 10.1016/j.ymeth.2020.09.009