title: Protein-driven inference of miRNA-disease associations.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a highly abundant class of non-coding RNA genes involved in cellular regulation and thus also diseases. Despite miRNAs being important disease factors, miRNA-disease associations remain low in number and of variable reliability. Furthermore, existing databases and prediction methods do not explicitly facilitate forming hypotheses about the possible molecular causes of the association, thereby making the path to experimental follow-up longer.
  
  
  RESULTS
  Here we present miRPD in which miRNA-Protein-Disease associations are explicitly inferred. Besides linking miRNAs to diseases, it directly suggests the underlying proteins involved, which can be used to form hypotheses that can be experimentally tested. The inference of miRNAs and diseases is made by coupling known and predicted miRNA-protein associations with protein-disease associations text mined from the literature. We present scoring schemes that allow us to rank miRNA-disease associations inferred from both curated and predicted miRNA targets by reliability and thereby to create high- and medium-confidence sets of associations. Analyzing these, we find statistically significant enrichment for proteins involved in pathways related to cancer and type I diabetes mellitus, suggesting either a literature bias or a genuine biological trend. We show by example how the associations can be used to extract proteins for disease hypothesis.
  
  
  METHODS
  All datasets, software and a searchable Web site are available at http://mirpd.jensenlab.org.
authors.affiliation: Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research and The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Mørk
authors.forename: Sune
authors.initials: S
authors.lastname: Pletscher-Frankild
authors.forename: Albert
authors.initials: A
authors.lastname: Palleja Caro
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
mesh_terms: D003920:Diabetes Mellitus / Q000235:genetics; D004194:Disease / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D035683:MicroRNAs; D011506:Proteins