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

Chagas, Vinicius S. ; Groeneveld, Clarice S. ; Oliveira, Kelin G. LU ; Trefflich, Sheyla ; de Almeida, Rodrigo C. ; Ponder, Bruce A.J. ; Meyer, Kerstin B. ; Jones, Steven J.M. ; Robertson, A. Gordon and Castro, Mauro A.A. (2019) In Bioinformatics 35(24). p.5357-5358
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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Bioinformatics
volume
35
issue
24
pages
2 pages
publisher
Oxford University Press
external identifiers
  • scopus:85077783404
  • pmid:31250887
ISSN
1367-4803
DOI
10.1093/bioinformatics/btz534
language
English
LU publication?
yes
id
925546db-3679-4ffd-864d-1d6bc26181c9
date added to LUP
2020-01-27 17:31:53
date last changed
2024-04-17 04:20:05
@article{925546db-3679-4ffd-864d-1d6bc26181c9,
  abstract     = {{<p>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.</p>}},
  author       = {{Chagas, Vinicius S. and Groeneveld, Clarice S. and Oliveira, Kelin G. and Trefflich, Sheyla and de Almeida, Rodrigo C. and Ponder, Bruce A.J. and Meyer, Kerstin B. and Jones, Steven J.M. and Robertson, A. Gordon and Castro, Mauro A.A.}},
  issn         = {{1367-4803}},
  language     = {{eng}},
  month        = {{12}},
  number       = {{24}},
  pages        = {{5357--5358}},
  publisher    = {{Oxford University Press}},
  series       = {{Bioinformatics}},
  title        = {{RTNduals an R/Bioconductor package for analysis of co-regulation and inference of dual regulons}},
  url          = {{http://dx.doi.org/10.1093/bioinformatics/btz534}},
  doi          = {{10.1093/bioinformatics/btz534}},
  volume       = {{35}},
  year         = {{2019}},
}