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Updated: Feb 3, 2026
Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm
Published on: January 28, 2011
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome
Tiago C Silva1,2, Simon G Coetzee1, Nicole Gull1
1Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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.
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