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

Bioinformatics 2019 Jun;35(11):1974-1977

Department 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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Source
https://academic.oup.com/bioinformatics/advance-article/doi/
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bty902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546131PMC
June 2019
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