AbstractMotivationDNA 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 packageELMER(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 ofELMERthat 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 this approach can identify GRNs associated with many new Master Regulators includingKLF5in breast cancer.AvailabilityELMERv.2 is available as an R/Bioconductor package athttp://bioconductor.org/packages/ELMER/
ComiRNet: a web-based system for the analysis of miRNA-gene regulatory networks
