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

被引：15

作者：

Chagas, Vinicius S. ^{[1
]}

Groeneveld, Clarice S. ^{[1
]}

Oliveira, Kelin G. ^{[1
,2
]}

Trefflich, Sheyla ^{[3
]}

de Almeida, Rodrigo C. ^{[4
]}

Ponder, Bruce A. J. ^{[5
,6
]}

Meyer, Kerstin B. ^{[5
,6
,7
]}

Jones, Steven J. M. ^{[8
]}

Robertson, A. Gordon ^{[8
]}

Castro, Mauro A. A. ^{[1
]}

机构：

[1] Univ Fed Parana, Bioinformat & Syst Biol Lab, BR-81520260 Curitiba, Parana, Brazil

[2] Lund Univ, Sect Oncol & Pathol, Dept Clin Sci, S-22185 Lund, Sweden

[3] Univ Fed Minas Gerais, Inst Biol Sci, Grad Program Bioinformat, BR-31270901 Belo Horizonte, MG, Brazil

[4] Leiden Univ, Dept Biomed Data Sci, Med Ctr, Mol Epidemiol, NL-2300 RC Leiden, Netherlands

[5] Univ Cambridge, Li Ka Shing Ctr, Dept Oncol, Cambridge CB2 0RE, England

[6] Univ Cambridge, Canc Res UK Cambridge Inst, Li Ka Shing Ctr, Cambridge CB2 0RE, England

[7] Wellcome Sanger Inst, Hinxton CB10 1SA, England

[8] BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada

来源：

BIOINFORMATICS | 2019年 / 35卷 / 24期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/btz534

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：5357 / 5358

页数：2

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