ArticleBioinformatics (Oxford, England)2019
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
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- Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.Scientific reports · 2025Article
- Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms.Bioinformatics (Oxford, England) · 2025Article
- Unraveling the intricate molecular landscape and potential biomarkers in lung adenocarcinoma through integrative epigenomic and transcriptomic profiling.Scientific reports · 2025Article
- Uncovering the epigenetic regulatory clues of PRRT1 in Alzheimer's disease: a strategy integrating multi-omics analysis with explainable machine learning.Alzheimer's research & therapy · 2025Article
- Integration of multi-omics layers empowers precision diagnosis through unveiling pathogenic mechanisms on maple syrup urine disease.Journal of inherited metabolic disease · 2025Article
17 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
motivationDNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set.
resultsWe present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that Supervised mode significantly increases statistical power and identifies additional GRNs and associated Master Regulators, such as SOX11 and KLF5 in Basal-like breast cancer. AVAILABILITY AND IMPLEMENTATION: ELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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