ArticleNucleic acids research2013
CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 61 citations in OpenAlex.
- Transcription factors that define the epigenome structures and transcriptomes in microglia.Experimental hematology · 2025Review
- DNA methylation in esophageal cancer: technological advances and early detection clinical applications.Frontiers in oncology · 2025Review
- HBCR_DMR: A Hybrid Method Based on Beta-Binomial Bayesian Hierarchical Model and Combination of Ranking Method to Detect Differential Methylation Regions in Bisulfite Sequencing Data.Journal of personalized medicine · 2024Article
- Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer.Clinical and translational medicine · 2022Article
- Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation.Nature metabolism · 2022Article
- Investigating Different DNA Methylation Patterns at the Resolution of Methylation Haplotypes.Frontiers in genetics · 2021Article
- Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease.Nature genetics · 2019Article
- Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species.Briefings in bioinformatics · 2019Article
- Hypomethylation in the promoter region ofArchives animal breeding · 2019Article
- A survey of the approaches for identifying differential methylation using bisulfite sequencing data.Briefings in bioinformatics · 2018Review
- Double signal enhancement strategy based on rolling circle amplification and photoinduced electron transfer for ultrasensitive fluorometric detection of methylated DNA.Mikrochimica acta · 2018Article
- DNA methylation in silkworm genome may provide insights into epigenetic regulation of response to Bombyx mori cypovirus infection.Scientific reports · 2017Article
- Article
- CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.Bioinformatics (Oxford, England) · 2017Article
- DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta.PloS one · 2017Article
- AgIn: measuring the landscape of CpG methylation of individual repetitive elements.Bioinformatics (Oxford, England) · 2016Article
- Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.Nucleic acids research · 2016Article
- Epigenetic Modulation of Human Podocyte Vitamin D Receptor in HIV Milieu.Journal of molecular biology · 2015Article
- Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types.Scientific reports · 2015Article
- Nonparametric Bayesian clustering to detect bipolar methylated genomic loci.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure. However, methods for large-scale identification of methylation patterns from bisulfite sequencing are lacking. We developed a comprehensive tool, CpG_MPs, for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conservatively and differentially methylated regions across paired or multiple samples (cells or tissues) are identified by combining a combinatorial algorithm with Shannon entropy. CpG_MPs identified large amounts of genomic regions with different methylation patterns across five human bisulfite sequencing data during cellular differentiation. Different sequence features and significantly cell-specific methylation patterns were observed. These potentially functional regions form candidate regions for functional analysis of DNA methylation during cellular differentiation. CpG_MPs is the first user-friendly tool for identifying methylation patterns of genomic regions from bisulfite sequencing data, permitting further investigation of the biological functions of genome-scale methylation patterns.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.