title: MIRTFnet: analysis of miRNA regulated transcription factors.
abstract: BACKGROUND
  Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed.
  
  
  RESULTS
  MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably.
  
  
  CONCLUSIONS
  The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis.
authors.affiliation: Institut für Informatik, Ludwig-Maximilians-Universität München, Germany.
authors.forename: Haroon
authors.initials: H
authors.lastname: Naeem
authors.forename: Robert
authors.initials: R
authors.lastname: Küffner
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008957:Models, Genetic; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors