RTNduals an R/Bioconductor package for analysis of co-regulation and inference of dual regulons

Research output: Contribution to journalLetter

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.

Details

Authors
  • Vinicius S. Chagas
  • Clarice S. Groeneveld
  • Kelin G. Oliveira
  • Sheyla Trefflich
  • Rodrigo C. de Almeida
  • Bruce A.J. Ponder
  • Kerstin B. Meyer
  • Steven J.M. Jones
  • A. Gordon Robertson
  • Mauro A.A. Castro
Organisations
External organisations
  • Federal University of Paraná
  • Federal University of Minas Gerais
  • Leiden University Medical Centre
  • University of Cambridge
  • Wellcome Trust Sanger Institute
  • British Columbia Cancer Agency
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Bioinformatics and Systems Biology
Original languageEnglish
Pages (from-to)5357-5358
Number of pages2
JournalBioinformatics (Oxford, England)
Volume35
Issue number24
Publication statusPublished - 2019 Dec 15
Publication categoryResearch
Peer-reviewedYes