Vinicius S Chagas1, Clarice S Groeneveld1, Kelin G Oliveira1,2, Sheyla Trefflich3, Rodrigo C de Almeida4, Bruce A J Ponder5, Kerstin B Meyer5,6, Steven J M Jones7, A Gordon Robertson7, Mauro A A Castro1. 1. Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil. 2. Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund 221 85, Sweden. 3. Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil. 4. Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands. 5. Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK. 6. Wellcome Sanger Institute, Hinxton CB10 1SA, UK. 7. Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver V5Z 4S6, Canada.
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 analyzing 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 AND IMPLEMENTATION: 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.
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 analyzing 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 AND IMPLEMENTATION: 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.
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