title: CoRegNet: reconstruction and integrated analysis of co-regulatory networks.
abstract: CoRegNet is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, CoRegNet can be used to: reconstruct a large-scale co-regulatory network, integrate regulation evidences such as transcription factor binding sites and ChIP data, estimate sample-specific regulator activity, identify cooperative transcription factors and analyze the sample-specific combinations of active regulators through an interactive visualization tool. In this study CoRegNet was used to identify driver regulators of bladder cancer.
  
  
  BACKGROUND
  CoRegNet is available at http://bioconductor.org/packages/CoRegNet
  
  
  BACKGROUND
  remy.nicolle@issb.genopole.fr or mohamed.elati@issb.genopole.fr
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.
authors.forename: Rémy
authors.initials: R
authors.lastname: Nicolle
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.
authors.forename: François
authors.initials: F
authors.lastname: Radvanyi
authors.affiliation: iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Elati
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D001749:Urinary Bladder Neoplasms / Q000235:genetics*
chemical_list: D014157:Transcription Factors