ArticleScientific reports2018
Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 49 citations in OpenAlex.
- Manganese (III) tetrakis (4-benzoic acid) porphyrin (MnTBAP) represses sulfide:quinone oxidoreductase expression and targets the sulfido-redox system in glioblastoma models.Redox report : communications in free radical research · 2025Article
- Unveiling Epigenetic Regulatory Elements Associated with Breast Cancer Development.International journal of molecular sciences · 2025Article
- Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors.Acta neuropathologica communications · 2024Article
- DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer.Clinical epigenetics · 2023Article
- Inference of epigenetic subnetworks by Bayesian regression with the incorporation of prior information.Scientific reports · 2022Article
- DNA methylation-based profiling reveals distinct clusters with survival heterogeneity in high-grade serous ovarian cancer.Clinical epigenetics · 2021Article
- The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes.Scientific reports · 2021Article
- Review
- Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications.International journal of molecular sciences · 2019Review
- Application of Fast Integration Strategy for Multi-Omics Data and Limited Random Forest Model in Survival Prediction of Glioblastoma.IET systems biologyArticle
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order to find clinically useful prognostic markers for glioma patients' survival, we employed Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID) algorithm on DNA methylation (HumanMethylation450 platform) and RNA-seq datasets from The Cancer Genome Atlas (TCGA) for 88 patients observed until death. The input features were ranked according to their importance in predicting patients' longer (400+ days) or shorter (≤400 days) survival without prior classification of the patients. Interestingly, out of the 65 most important features found, 63 are methylation sites, and only two mRNAs. Moreover, 61 out of the 63 methylation sites are among those detected by the 450 k array technology, while being absent in the HumanMethylation27. The most important methylation feature (cg15072976) overlaps with the RE1 Silencing Transcription Factor (REST) binding site, and was confirmed to intersect with the REST binding motif in human U87 glioma cells. Six additional methylation sites from the top 63 overlap with REST sites. We found that the methylation status of the cg15072976 site affects transcription factor binding in U87 cells in gel shift assay. The cg15072976 methylation status discriminates ≤400 and 400+ patients in an independent dataset from TCGA and shows positive association with survival time as evidenced by Kaplan-Meier plots.
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