ArticleGenome biology2015
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
What it found
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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
126 citing papers in PubMed, 218 citations in OpenAlex.
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- Methods for analysing wildlife DNA methylation data.Conservation physiology · 2026Article
- KnowYourCG: Facilitating base-level sparse methylome interpretation.Science advances · 2025Article
- CTCF Mediates the Cis-Regulatory Hubs in Mouse Hearts.International journal of molecular sciences · 2025Article
- Cell-free DNA-based inference of the activities of 370 + transcription factors mirrors their activities in tumors.BMC genomics · 2025Article
- Integrative multi-omics analysis decodes HOXC9-driven malignant transformation and metastasis in OSCC.iScience · 2025Article
- Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.Bioinformatics (Oxford, England) · 2025Article
- Dissecting the Emerging Regulatory and Mechanistic Paradigms of Transcribed Conserved Non-Coding Elements in Breast Cancer.Biomolecules · 2025Article
- Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms.Bioinformatics (Oxford, England) · 2025Article
- Genome-wide DNA methylation regulation analysis provides novel insights on post-radiation breast cancer.Scientific reports · 2025Article
- Genome-wide association studies are enriched for interacting genes.BioData mining · 2025Article
- Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays.Epigenetics · 2024Article
- Genome wide association studies are enriched for interacting genes.Research square · 2024Article
- DNA methylation clocks for estimating biological age in Chinese cohorts.Protein & cell · 2024Article
- MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.Nature communications · 2024Article
- Activation of Bivalent Gene POU4F1 Promotes and Maintains Basal-like Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma.Cell death & disease · 2024Article
- Liquid biopsy in T-cell lymphoma: biomarker detection techniques and clinical application.Molecular cancer · 2024Review
66 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
Recent studies indicate that DNA methylation can be used to identify transcriptional enhancers, but no systematic approach has been developed for genome-wide identification and analysis of enhancers based on DNA methylation. We describe ELMER (Enhancer Linking by Methylation/Expression Relationships), an R-based tool that uses DNA methylation to identify enhancers and correlates enhancer state with expression of nearby genes to identify transcriptional targets. Transcription factor motif analysis of enhancers is coupled with expression analysis of transcription factors to infer upstream regulators. Using ELMER, we investigated more than 2,000 tumor samples from The Cancer Genome Atlas. We identified networks regulated by known cancer drivers such as GATA3 and FOXA1 (breast cancer), SOX17 and FOXA2 (endometrial cancer), and NFE2L2, SOX2, and TP63 (squamous cell lung cancer). We also identified novel networks with prognostic associations, including RUNX1 in kidney cancer. We propose ELMER as a powerful new paradigm for understanding the cis-regulatory interface between cancer-associated transcription factors and their functional target genes.
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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.