ArticleBMC bioinformatics2020
Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Epigenetic Alterations in Inborn Errors of Immunity.Journal of clinical medicine · 2022Review
- The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundGenome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells, ESCs exhibit varying degrees of pluripotency, and epigenetic changes occurring in this process have emerged as important factors explaining stem cell pluripotency.
resultsHere, using paired scBS-seq and scRNA-seq data of mice, we constructed a machine learning model that predicts degrees of pluripotency for mouse ESCs. Since the biological activities of non-CpG markers have yet to be clarified, we tested the predictive power of CpG and non-CpG markers, as well as a combination thereof, in the model. Through rigorous performance evaluation with both internal and external validation, we discovered that a model using both CpG and non-CpG markers predicted the pluripotency of ESCs with the highest prediction performance (0.956 AUC, external test). The prediction model consisted of 16 CpG and 33 non-CpG markers. The CpG and most of the non-CpG markers targeted depletions of methylation and were indicative of cell pluripotency, whereas only a few non-CpG markers reflected accumulations of methylation. Additionally, we confirmed that there exists the differing pluripotency between individual developmental stages, such as E3.5 and E6.5, as well as between induced mouse pluripotent stem cell (iPSC) and somatic cell.
conclusionsIn this study, we investigated CpG and non-CpG methylation in relation to mouse stem cell pluripotency and developed a model thereon that successfully predicts the pluripotency of mouse ESCs.
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Registered trials
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