title: miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data.
abstract: BACKGROUND
  Algorithms predicting microRNA (miR)-mRNA interactions generate high numbers of possible interactions, many of which might be non-existent or irrelevant in a certain biological context. It is desirable to develop a transparent, user-friendly, unbiased tool to enrich miR-mRNA predictions.
  
  
  RESULTS
  The miMsg algorithm uses matched miR/mRNA expression data to enrich miR-mRNA predictions. It grades interactions by the number, magnitude and significance of misplacements in the combined ranking profiles of miR/mRNA expression assessed over multiple biological samples. miMsg requires minimal user input and makes no statistical assumptions. It identified 921 out of 56 262 interactions as top scoring and significant in an actual germ cell cancer dataset. Twenty-eight miR-mRNA pairs were deemed of highest interest based on ranking by miMsg and supported by current knowledge about validated interactions and biological function. To conclude, miMsg is an effective algorithm to reduce a high number of predicted interactions to a small set of high confidence interactions for further study.
  
  
  METHODS
  Matlab source code and datasets available at www.martinrijlaarsdam.nl/mimsg .
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Pathology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands. l.looijenga@erasmusmc.nl
authors: Martin A
authors: MA
authors: Rijlaarsdam
authors: David J
authors: DJ
authors: Rijlaarsdam
authors: Ad J M
authors: AJ
authors: Gillis
authors: Lambert C J
authors: LC
authors: Dorssers
authors: Leendert H J
authors: LH
authors: Looijenga
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D009373:Neoplasms, Germ Cell and Embryonal / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger