Dataset Information
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.
Ontology highlight
ABSTRACT: 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.
SUBMITTER: Silva TC
PROVIDER: S-EPMC6546131 | biostudies-literature | 2019 Jun
REPOSITORIES: biostudies-literature
Publications
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.
Bioinformatics (Oxford, England) 20190601 11
<h4>Motivation</h4>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.<h4>Results</h4>We present a completely r ...[more]