title: Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.
abstract: BACKGROUND
  There have been many successful experimental and bioinformatics efforts to elucidate transcription factor (TF)-target networks in several organisms. For many organisms, these annotations are complemented by miRNA-target networks of good quality. Attempts that use these networks in combination with gene expression data to draw conclusions on TF or miRNA activity are, however, still relatively sparse.
  
  
  RESULTS
  In this study, we propose Bayesian inference of regulation of transcriptional activity (BIRTA) as a novel approach to infer both, TF and miRNA activities, from combined miRNA and mRNA expression data in a condition specific way. That means our model explains mRNA and miRNA expression for a specific experimental condition by the activities of certain miRNAs and TFs, hence allowing for differentiating between switches from active to inactive (negative switch) and inactive to active (positive switch) forms. Extensive simulations of our model reveal its good prediction performance in comparison to other approaches. Furthermore, the utility of BIRTA is demonstrated at the example of Escherichia coli data comparing aerobic and anaerobic growth conditions, and by human expression data from pancreas and ovarian cancer.
  
  
  METHODS
  The method is implemented in the R package birta, which is freely available for Bio-conductor (>=2.10) on http://www.bioconductor.org/packages/release/bioc/html/birta.html.
authors.affiliation: Ludwig-Maximilians-Universität München, Gene Center Munich and Center for integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Feodor-Lynen-Street 25, 81377 Munich, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.forename: Khalid
authors.initials: K
authors.lastname: Abnaof
authors.forename: Stephan
authors.initials: S
authors.lastname: Gade
authors.forename: Erfan
authors.initials: E
authors.lastname: Younesi
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
authors.forename: Holger
authors.initials: H
authors.lastname: Fröhlich
mesh_terms: D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D010051:Ovarian Neoplasms / Q000235:genetics / Q000378:metabolism; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors