ArticlePloS one2015
Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 35 citations in OpenAlex.
- MRI phenotypes of the brain are related to future stroke and mortality in patients with manifest arterial disease: The SMART-MR study.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2020Trial
- Statistical relationships across epigenomes using large-scale hierarchical clustering.Bioinformatics advances · 2025Article
- Examining the Effects of Environment, Geography, and Elevation on Patterns of DNA Methylation Across Populations of Two Widespread Bumble Bee Species.Genome biology and evolution · 2024Article
- Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis.NAR cancer · 2024Article
- Identification of Distinct Brain MRI Phenotypes and Their Association With Long-Term Dementia Risk in Community-Dwelling Older Adults.Neurology · 2024Article
- Article
- Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine.Biochimica et biophysica acta. Reviews on cancer · 2021Review
- Progression Risk Score Estimation Based on Immunostaining Data in Oral Cancer Using Unsupervised Hierarchical Clustering Analysis: A Retrospective Study in Taiwan.Journal of personalized medicine · 2021Article
- Phenomapping of Patients with Primary Breast Cancer Using Machine Learning-Based Unsupervised Cluster Analysis.Journal of personalized medicine · 2021Article
- Methylated biomarkers for breast cancer identified through public database analysis and plasma target capture sequencing.Annals of translational medicine · 2021Article
- Accurate and efficient detection of gene fusions from RNA sequencing data.Genome research · 2021Article
- Identification of ZG16B as a prognostic biomarker in breast cancer.Open medicine (Warsaw, Poland) · 2021Article
- Circulating plasma lncRNAs as novel markers of EGFR mutation status and monitors of epidermal growth factor receptor-tyrosine kinase inhibitor therapy.Thoracic cancer · 2020Article
- High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
- HOPX homeobox methylation in differentiated thyroid cancer and its clinical relevance.Endocrine connections · 2018Article
- A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.Genome biology · 2018Article
- Decreased methylation in the SNAI2 and ADAM23 genes associated with de-differentiation and haematogenous dissemination in breast cancers.BMC cancer · 2018Article
- Large-scale analysis ofClinical epigenetics · 2018Article
- Xist reduction in breast cancer upregulates AKT phosphorylation via HDAC3-mediated repression of PHLPP1 expression.Oncotarget · 2016Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.
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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.