ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

• Published in: Bioinformatics (Oxford, England) Vol. 35; no. 11; pp. 1974 - 1977
• Main Authors: Silva, Tiago C, Coetzee, Simon G, Gull, Nicole, Yao, Lijing, Hazelett, Dennis J, Noushmehr, Houtan, Lin, De-Chen, Berman, Benjamin P
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.06.2019
• Subjects: Applications Notes
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/bty902

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. 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. ELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/. Supplementary data are available at Bioinformatics online.