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  • Chagas, Vinicius S.Federal University of Paraná (author)

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

  • Article/chapterEnglish2019

Publisher, publication year, extent ...

  • 2019-06-28
  • Oxford University Press (OUP),2019
  • 2 s.

Numbers

  • LIBRIS-ID:oai:lup.lub.lu.se:925546db-3679-4ffd-864d-1d6bc26181c9
  • https://lup.lub.lu.se/record/925546db-3679-4ffd-864d-1d6bc26181c9URI
  • https://doi.org/10.1093/bioinformatics/btz534DOI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Groeneveld, Clarice S.Federal University of Paraná (author)
  • Oliveira, Kelin G.Lund University,Lunds universitet,Tumörmikromiljön,Forskargrupper vid Lunds universitet,Tumor microenvironment,Lund University Research Groups,Federal University of Paraná(Swepub:lu)ke4436de (author)
  • Trefflich, SheylaFederal University of Minas Gerais (author)
  • de Almeida, Rodrigo C.Leiden University Medical Centre (author)
  • Ponder, Bruce A.J.University of Cambridge (author)
  • Meyer, Kerstin B.University of Cambridge,Wellcome Trust Sanger Institute (author)
  • Jones, Steven J.M.British Columbia Cancer Agency (author)
  • Robertson, A. GordonBritish Columbia Cancer Agency (author)
  • Castro, Mauro A.A.Federal University of Paraná (author)
  • Federal University of ParanáTumörmikromiljön (creator_code:org_t)

Related titles

  • In:Bioinformatics: Oxford University Press (OUP)35:24, s. 5357-53581367-48031367-4811

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