ArticlePhysiological genomics2013
Detection of differentially methylated gene promoters in failing and nonfailing human left ventricle myocardium using computation analysis.
Article in Physiological genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
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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
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 60 citations in OpenAlex.
- A stop-gain variant inHGG advances · 2023Pooled it
- Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology.PLoS computational biology · 2022Pooled it
- Alogliptin Reduces Oxidative Stress in Cardiomyocytes and Ameliorates Diabetic Cardiomyopathy via the AURKB/NLGN2 Signaling.The Kaohsiung journal of medical sciences · 2026Article
- Epigenome-wide association study for dilated cardiomyopathy in left ventricular heart tissue identifies putative gene sets associated with cardiac pathology and early indicators of cardiac risk.Clinical epigenetics · 2025Article
- Regulatory mechanisms of mAmerican journal of translational research · 2025Review
- Changes in DNA methylation associated with a specific mode of delivery: a pilot study.Frontiers in medicine · 2024Article
- LncRNA CALML3-AS1 modulated by mCancer gene therapy · 2023Article
- Integration of epigenetic regulatory mechanisms in heart failure.Basic research in cardiology · 2023Review
- Effect of mechanical unloading on genome-wide DNA methylation profile of the failing human heart.JCI insight · 2023Article
- Development and verification of the nomogram for dilated cardiomyopathy gene diagnosis.Scientific reports · 2022Article
- Methylation status of TK1 correlated with immune infiltrates in prostate cancer.Frontiers in genetics · 2022Article
- Epigenetic Regulation of Endothelial Cell Function by Nucleic Acid Methylation in Cardiac Homeostasis and Disease.Cardiovascular drugs and therapy · 2021Review
- Mitochondria signaling to the epigenome: A novel role for an old organelle.Free radical biology & medicine · 2021Review
- In situ nuclear DNA methylation in dilated cardiomyopathy: an endomyocardial biopsy study.ESC heart failure · 2020Article
- Epigenetics in dilated cardiomyopathy.Current opinion in cardiology · 2019Review
- Epigenetic Biomarkers in Cardiovascular Diseases.Frontiers in genetics · 2019Review
- Increased Cardiac Arrhythmogenesis Associated With Gap Junction Remodeling With Upregulation of RNA-Binding Protein FXR1.Circulation · 2018Article
- Translational Perspective on Epigenetics in Cardiovascular Disease.Journal of the American College of Cardiology · 2017Review
- Methods to increase reproducibility in differential gene expression via meta-analysis.Nucleic acids research · 2017Article
- Knockdown of DNA methyltransferase 3a alters gene expression and inhibits function of embryonic cardiomyocytes.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2016Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
Human dilated cardiomyopathy (DCM) is characterized by congestive heart failure and altered myocardial gene expression. Epigenetic changes, including DNA methylation, are implicated in the development of DCM but have not been studied extensively. Clinical human DCM and nonfailing control left ventricle samples were individually analyzed for DNA methylation and expressional changes. Expression microarrays were used to identify 393 overexpressed and 349 underexpressed genes in DCM (GEO accession number: GSE43435). Gene promoter microarrays were utilized for DNA methylation analysis, and the resulting data were analyzed by two different computational methods. In the first method, we utilized subtractive analysis of DNA methylation peak data to identify 158 gene promoters exhibiting DNA methylation changes that correlated with expression changes. In the second method, a two-stage approach combined a particle swarm optimization feature selection algorithm and a discriminant analysis via mixed integer programming classifier to identify differentially methylated gene promoters. This analysis identified 51 hypermethylated promoters and six hypomethylated promoters in DCM with 100% cross-validation accuracy in the group assignment. Generation of a composite list of genes identified by subtractive analysis and two-stage computation analysis revealed four genes that exhibited differential DNA methylation by both methods in addition to altered gene expression. Computationally identified genes (AURKB, BTNL9, CLDN5, and TK1) define a central set of differentially methylated gene promoters that are important in classifying DCM. These genes have no previously reported role in DCM. This study documents that rigorous computational analysis applied to microarray analysis of healthy and diseased human heart samples helps to define clinically relevant DNA methylation and expressional changes in DCM.
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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.