Authors:
VS Chagas, CS Groeneveld, KG Oliveira, S Trefflich, RC de Almeida, BAJ Ponder, KB Meyer, SJM Jones, AG Robertson, MAA Castro
Journal name: 
Bioinformatics
Abstract: 
MOTIVATION: Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analysing pairs of regulons. RESULTS: RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts. AVAILABILITY: RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
DOI: 
http://doi.org/10.1093/bioinformatics/btz534
Research group: 
Ponder Group
E-pub date: 
31 May 2019
Users with this publication listed: 
Bruce Ponder