ArticleBMC bioinformatics2014
Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed, 23 citations in OpenAlex.
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- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach.Methods in molecular biology (Clifton, N.J.) · 2021Article
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- Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation.Molecular neurobiology · 2018Article
- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
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- Nucleotide diversity analysis highlights functionally important genomic regions.Scientific reports · 2016Article
- The mysterious orphans of Mycoplasmataceae.Biology direct · 2016Article
- Gene Evolutionary Trajectories and GC Patterns Driven by Recombination inFrontiers in plant science · 2016Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up to many samples. It is therefore useful to develop computational prediction methods for DNA methylation. Our previous studies highlighted the existence of correlations between the GC content of the third codon position (GC₃), methylation, and gene expression. We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data.
resultsWe first derive equations to describe the relationship between gene methylation levels, GC₃, expression, length, and other gene compositional features. We next assess gene compositional features involving sixmers and their association with methylation levels and other gene level properties. By applying our sixmer-based approach on rice gene expression data we show that it can accurately predict methylation (Pearson's correlation coefficient r = 0.79) for the majority (79%) of the genes. Matlab code with our model is included.
conclusionsGene expression variation can be used as predictors of gene methylation levels.
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Registered trials
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.