ArticleBMC genomics2017
Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 60 citations in OpenAlex.
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- Molecular mechanisms of multi-omic regulation in breast cancer.Frontiers in oncology · 2023Review
- Epigenetic liquid biopsies for minimal residual disease, what's around the corner?Frontiers in oncology · 2023Review
- Identify potential driver genes for PAX-FOXO1 fusion-negative rhabdomyosarcoma through frequent gene co-expression network mining.Frontiers in oncology · 2023Article
- Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients.Clinical epigenetics · 2022Article
- Association between cancer genes and germ layer specificity.Medical oncology (Northwood, London, England) · 2022Article
- Construction of the coexpression network involved in the pathogenesis of thyroid eye disease via bioinformatics analysis.Human genomics · 2022Article
- Hypermethylation of tumor suppressor lncRNA MEF2C-AS1 frequently happened in patients at all stages of colorectal carcinogenesis.Clinical epigenetics · 2022Article
- Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers.BMC genomic data · 2022Article
- DNA methylation-based predictors of health: applications and statistical considerations.Nature reviews. Genetics · 2022Review
- Synergy between the Levels of Methylation of microRNA Gene Sets in Primary Tumors and Metastases of Ovarian Cancer Patients.Bulletin of experimental biology and medicine · 2022Article
- Thorough statistical analyses of breast cancer co-methylation patterns.BMC genomic data · 2022Article
- Functional impact of multi-omic interactions in breast cancer subtypes.Frontiers in genetics · 2022Article
- TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.Genomics, proteomics & bioinformatics · 2021Article
- TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery.BMC bioinformatics · 2021Article
- ZNF471 modulates EMT and functions as methylation regulated tumor suppressor with diagnostic and prognostic significance in cervical cancer.Cell biology and toxicology · 2021Article
- Genomic Biomarkers of Meningioma: A Focused Review.International journal of molecular sciences · 2021Review
- MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks.NPJ systems biology and applications · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation is the major form of epigenetic modifications through which the cell regulates the gene expression and silencing. There have been extensive studies on the roles of DNA methylation in cancers, and several cancer drugs were developed targeting this process. However, DNA co-methylation cluster has not been examined in depth, and co-methylation in multiple cancer types has never been studied previously.
resultsIn this study, we applied newly developed lmQCM algorithm to mine co-methylation clusters using methylome data from 11 cancer types in TCGA database, and found frequent co-methylated gene clusters exist in these cancer types. Among the four identified frequent clusters, two of them separate the tumor sample from normal sample in 10 out of 11 cancer types, which indicates that consistent epigenetic landscape changes exist in multiple cancer types.
conclusionThis discovery provides new insight on the epigenetic regulation in cancers and leads to potential new direction for epigenetic biomarker and cancer drug discovery. We also found that genes commonly believed to be silenced via hypermethylation in cancers may still display highly variable methylation levels among cancer cells, and should be considered while using them as epigenetic biomarkers.
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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.