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- Title
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.
- Authors
Silva, Tiago C; Coetzee, Simon G; Gull, Nicole; Yao, Lijing; Hazelett, Dennis J; Noushmehr, Houtan; Lin, De-Chen; Berman, Benjamin P
- 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.
- Subjects
GENE regulatory networks; GENE enhancers; STATISTICAL power analysis; DNA methylation; GENE expression
- Publication
Bioinformatics, 2019, Vol 35, Issue 11, p1974
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bty902