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

Tiago C. Silva | Zendy; Simon G. Coetzee | Zendy; Nicole Gull | Zendy; Lijing Yao | Zendy; Dennis J. Hazelett | Zendy; Houtan Noushmehr | Zendy; DeChen Lin | Zendy; Benjamin P. Berman | Zendy

Open Access

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

Author(s) -

Tiago C. Silva,

Simon G. Coetzee,

Nicole Gull,

Lijing Yao,

Dennis J. Hazelett,

Houtan Noushmehr,

DeChen Lin,

Benjamin P. Berman

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty902

Subject(s) - bioconductor , transcriptome , dna methylation , computational biology , biology , methylation , gene , genetics , dna , gene regulatory network , gene expression

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.

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