ArticleNucleic acids research2016
A computational method for studying the relation between alternative splicing and DNA methylation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Predictive value of hepatic, hematological, and immunological markers and their temporal dynamics in chronic hepatitis B functional cure.Microbiology spectrum · 2025Article
- Trends of genetic contributions on epigenetic clocks and related methylation sites with aging: A population-based adult twin study.Aging cell · 2025Article
- DNA methylation may partly explain psychotropic drug-induced metabolic side effects: results from a prospective 1-month observational study.Clinical epigenetics · 2024Observational
- Identification of functional lncRNAs in atrial fibrillation based on RNA sequencing.BMC cardiovascular disorders · 2023Article
- A Novel EYA1 Mutation Causing Alternative RNA Splicing in a Chinese Family With Branchio-Oto Syndrome: Implications for Molecular Diagnosis and Clinical Application.Clinical and experimental otorhinolaryngology · 2023Article
- Differential exon usage of developmental genes is associated with deregulated epigenetic marks.Scientific reports · 2023Article
- Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep.Environmental epigenetics · 2023Article
- Paternal diet induces transgenerational epigenetic inheritance of DNA methylation signatures and phenotypes in sheep model.PNAS nexus · 2022Article
- ClickGene: an open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration.BioData mining · 2019Article
- Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling.BMC genomics · 2018Article
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation patterns and allows to correlate these patterns with inclusion propensity of exons. Pattern detection is based on dynamic time warping (DTW) of methylation profiles, a sophisticated similarity measure for signals that can be non-trivially transformed. We design a flexible self-organizing map approach to pattern grouping. Exemplary application on available data sets indicates that stable patterns which correlate non-trivially with exon inclusion do indeed exist. To improve the reliability of these predictions, further studies on larger data sets will be required. We have thus taken great care that our software runs efficiently on modern hardware, so that it can support future studies on large-scale data sets.
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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.