Title

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

Document Type

Article

Publication Date

6-1-2019

Publication Title

Bioinformatics (Oxford, England)

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.

PubMed ID

30364927

Volume

35

Issue

11

First Page

1974

Last Page

1977

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