ArticlePLoS computational biology2014
The dynamics of DNA methylation covariation patterns in carcinogenesis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 55 citations in OpenAlex.
- Aberrant Methylation of RASSF1A Closely Associated with HNSCC, a Meta-Analysis.Scientific reports · 2016Pooled it
- Embracing non-linearity in human ageing.Nature reviews. Genetics · 2026Review
- Evaluating the cross-reactivity of a stool methylated syndecan-2 (meJournal of gastrointestinal oncology · 2025Article
- EpiAge: a next-generation sequencing-basedAging · 2025Article
- On epigenetic stochasticity, entropy and cancer risk.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.PLoS computational biology · 2023Article
- The Mouse Papillomavirus Epigenetic Signature Is Characterised by DNA Hypermethylation after Lesion Regression.Viruses · 2021Article
- Article
- Origins of human disease: the chrono-epigenetic perspective.Nature reviews. Genetics · 2021Review
- Statistical mechanics meets single-cell biology.Nature reviews. Genetics · 2021Review
- An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome.Clinical and translational medicine · 2021Article
- Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease.Nature communications · 2021Article
- A fast score test for generalized mixture models.Biometrics · 2020Article
- Quantitative comparison of within-sample heterogeneity scores for DNA methylation data.Nucleic acids research · 2020Article
- Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data.BMC bioinformatics · 2019Article
- Tracking myeloid malignancies by targeted analysis of successive DNA methylation at neighboring CG dinucleotides.Haematologica · 2019Article
- Identifying pre-disease signals before metabolic syndrome in mice by dynamical network biomarkers.Scientific reports · 2019Article
- The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region.Scientific reports · 2019Article
- Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
- Statistical and integrative system-level analysis of DNA methylation data.Nature reviews. Genetics · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently it has been observed that cancer tissue is characterised by an increased variability in DNA methylation patterns. However, how the correlative patterns in genome-wide DNA methylation change during the carcinogenic progress has not yet been explored. Here we study genome-wide inter-CpG correlations in DNA methylation, in addition to single site variability, during cervical carcinogenesis. We demonstrate how the study of changes in DNA methylation covariation patterns across normal, intra-epithelial neoplasia and invasive cancer allows the identification of CpG sites that indicate the risk of neoplastic transformation in stages prior to neoplasia. Importantly, we show that the covariation in DNA methylation at these risk CpG loci is maximal immediately prior to the onset of cancer, supporting the view that high epigenetic diversity in normal cells increases the risk of cancer. Consistent with this, we observe that invasive cancers exhibit increased covariation in DNA methylation at the risk CpG sites relative to normal tissue, but lower levels relative to pre-cancerous lesions. We further show that the identified risk CpG sites undergo preferential DNA methylation changes in relation to human papilloma virus infection and age. Results are validated in independent data including prospectively collected samples prior to neoplastic transformation. Our data are consistent with a phase transition model of carcinogenesis, in which epigenetic diversity is maximal prior to the onset of cancer. The model and algorithm proposed here may allow, in future, network biomarkers predicting the risk of neoplastic transformation to be identified.
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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.