ArticleEpigenetics & chromatin2022
Pan-cancer predictions of transcription factors mediating aberrant DNA methylation.
Article in Epigenetics & chromatin, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- nanoASM: Long-Read Allele-Specific DNA Methylation Profiling Enables Functional Annotation of Regulatory Noncoding Variants in Human Prostate Tissues.bioRxiv : the preprint server for biology · 2026Article
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- Steroidogenic Acute Regulatory Protein in Breast Cancer: Mechanistic Insights into Pathogenesis and Therapeutics.International journal of molecular sciences · 2026Review
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- Navigating the complexities of epigenetic dysregulation in breast cancer and its implication in therapeutic interventions: a comprehensive overview.Molecular and cellular biochemistry · 2026Review
- Epigenetic control of metabolic identity across cell types.BMC genomics · 2025Article
- Helix pomatia agglutinin bound to surface glycans of small extracellular vesicles in-vitro and in-vivo increases in early and late stage breast cancer.Breast cancer (Tokyo, Japan) · 2025Article
- Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.Bioinformatics (Oxford, England) · 2025Article
- Th17-associated cytokine gene hypomethylation reflects epigenetic dysregulation in graves' disease.Frontiers in immunology · 2025Article
- MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets.Nucleic acids research · 2024Article
- MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns.Nucleic acids research · 2024Article
- Absence of GATA3/FOXA1 co-expression predicts poor prognosis in upper tract urothelial carcinoma.Frontiers in oncology · 2024Article
- Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications.Clinical epigenetics · 2023Article
- RBM10 Is a Biomarker Associated with Pan-Cancer Prognosis and Immune Infiltration: System Analysis Combined with In Vitro and Vivo Experiments.Oxidative medicine and cellular longevity · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAberrant DNA methylation is a hallmark of cancer cells. However, the mechanisms underlying changes in DNA methylation remain elusive. Transcription factors initially thought to be repressed from binding by DNA methylation, have recently emerged as being able to shape DNA methylation patterns.
resultsHere, we integrated the massive amount of data available from The Cancer Genome Atlas to predict transcription factors driving aberrant DNA methylation in 13 cancer types. We identified differentially methylated regions between cancer and matching healthy samples, searched for transcription factor motifs enriched in those regions and selected transcription factors with corresponding changes in gene expression. We predict transcription factors known to be involved in cancer as well as novel candidates to drive hypo-methylated regions such as FOXA1 and GATA3 in breast cancer, FOXA1 and TWIST1 in prostate cancer and NFE2L2 in lung cancer. We also predict transcription factors that lead to hyper-methylated regions upon transcription factor loss such as EGR1 in several cancer types. Finally, we validate that FOXA1 and GATA3 mediate hypo-methylated regions in breast cancer cells.
conclusionOur work highlights the importance of some transcription factors as upstream regulators shaping DNA methylation patterns in cancer.
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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.