Motivation: DNA 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. Results: We 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.
CITATION STYLE
Silva, T. C., Coetzee, S. G., Gull, N., Yao, L., Hazelett, D. J., Noushmehr, H., … Berman, B. P. (2019). ELmer v.2: An r/bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics, 35(11), 1974–1977. https://doi.org/10.1093/bioinformatics/bty902
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