title: mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data.
abstract: BACKGROUND
  Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation.
  
  
  RESULTS
  To facilitate the application of this approach we have created the mBISON web-application. mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3'UTR length. The tool can be accessed from the following web-resource: http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home .
  
  
  CONCLUSIONS
  mBISON is a web-application that helps to extract functional information about miRNAs from gene lists, which is in contrast to comparable applications easy to use by everyone and can be applied on ChIP-seq data directly.
authors.affiliation: Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany. marie.gebhardt@mdc-berlin.de.
authors.forename: Marie Luise
authors.initials: ML
authors.lastname: Gebhardt
authors.affiliation: Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany. arvind.mer@ki.se.|Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden. arvind.mer@ki.se.
authors.forename: Arvind Singh
authors.initials: AS
authors.lastname: Mer
authors.affiliation: Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany. andrade@uni-mainz.de.|Institute of Molecular Biology, Mainz, 55128, Germany. andrade@uni-mainz.de.|Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, 55128, Germany. andrade@uni-mainz.de.
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Andrade-Navarro
mesh_terms: D047369:Chromatin Immunoprecipitation; D020407:Internet; D035683:MicroRNAs / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs