ArticleBioinformatics (Oxford, England)2015
MethylMix: an R package for identifying DNA methylation-driven genes.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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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.
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Who cites it
95 citing papers in PubMed, 165 citations in OpenAlex.
- Macrophages transfer functional proteins to their surface during live-cell uptake.Nature chemical biology · 2026Article
- DNA methylation driven genes shape prognosis and tumor immune landscape in rectal cancer.Discover oncology · 2026Article
- High Expression of BTN3A3 Acts as an Independent Predictive Factor of Better Prognosis in Patients with Sarcomas.Cancer management and research · 2026Article
- Response to Antiangiogenic Therapy Is Associated with AIMP Protein Family Expression in Glioblastoma and Lower-Grade Gliomas.Cancer research communications · 2025Article
- A review on multi-omics integration for aiding study design of large scale TCGA cancer datasets.BMC genomics · 2025Review
- Clinical and Multiomic Features Differentiate Young Black and White Breast Cancer Cohorts Derived by Machine Learning Approaches.Clinical breast cancer · 2025Article
- Comprehensive Analysis Based on the TCGA Database Identified SCIN as a Key DNA Methylation-Driver Gene in Epstein-Barr Virus-Associated Gastric Cancer.Biochemical genetics · 2025Article
- Integrated analysis of methylation and transcriptome identifies a novel risk model for diagnosis, prognosis, and immune characteristics in head and neck squamous cell carcinoma.Molecular genetics and genomics : MGG · 2024Article
- Identifying a Risk Signature of Methylation-Driven Genes as a Predictor of Survival Outcome for Colon Cancer Patients.Applied biochemistry and biotechnology · 2024Article
- Analysis of methylation-driven genes for predicting the prognosis of patients with oral squamous cell carcinoma.Translational cancer research · 2024Article
- Comprehensive data mining reveals RTK/RAS signaling pathway as a promoter of prostate cancer lineage plasticity through transcription factors and CNV.Scientific reports · 2024Article
- Abnormal methylation mediated upregulation of LINC00857 boosts malignant progression of lung adenocarcinoma by modulating the miR-486-5p/NEK2 axis.The clinical respiratory journal · 2024Article
- A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma.Journal of molecular neuroscience : MN · 2024Article
- Machine Learning Methods for Gene Selection in Uveal Melanoma.International journal of molecular sciences · 2024Article
- Construction of a prognostic prediction model in liver cancer based on genes involved in integrin cell surface interactions pathway by multi-omics screening.Frontiers in cell and developmental biology · 2024Article
- Development of a prognostic model for early-stage gastric cancer-related DNA methylation-driven genes and analysis of immune landscape.Frontiers in molecular biosciences · 2024Article
- Identification of colon cancer subtypes based on multi-omics data-construction of methylation markers for immunotherapy.Frontiers in oncology · 2024Article
- Identifying key multifunctional components shared by critical cancer and normal liver pathways via SparseGMM.Cell reports methods · 2023Article
- A novel DNA methylation-driver gene signature for long-term survival prediction of hepatitis-positive hepatocellular carcinoma patients.Cancer medicine · 2022Article
- Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
unlabelledDNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is an alternative mechanism to deregulate gene expression in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. Yet, few tools exist that can formally identify hypo and hypermethylated genes that are predictive of transcription and thus functionally relevant for a particular disease. To accommodate this lack of tools, we developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix introduces a novel metric, the 'Differential Methylation value' or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data are used to identify, besides differential, transcriptionally predictive methylation states by focusing on methylation changes that effect gene expression. AVAILABILITY AND IMPLEMENTATION: MethylMix was implemented as an R package and is available in bioconductor.
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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.