title: Improving microRNA target prediction with gene expression profiles.
abstract: Mammalian genomes encode for thousands of microRNAs, which can potentially regulate the majority of protein-coding genes. They have been implicated in development and disease, leading to great interest in understanding their function, with computational methods being widely used to predict their targets. Most computational methods rely on sequence features, thermodynamics, and conservation filters; essentially scanning the whole transcriptome to predict one set of targets for each microRNA. This has the limitation of not considering that the same microRNA could have different sets of targets, and thus different functions, when expressed in different types of cells.
  
  
  
  To address this problem, we combine popular target prediction methods with expression profiles, via machine learning, to produce a new predictor: TargetExpress. Using independent data from microarrays and high-throughput sequencing, we show that TargetExpress outperforms existing methods, and that our predictions are enriched in functions that are coherent with the added expression profile and literature reports.
  
  
  
  Our method should be particularly useful for anyone studying the functions and targets of miRNAs in specific tissues or cells. TargetExpress is available at: http://targetexpress.ceiabreulab.org/ .
authors.affiliation: Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México.
authors.forename: Cesaré
authors.initials: C
authors.lastname: Ovando-Vázquez
authors.affiliation: Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México.
authors.forename: Daniel
authors.initials: D
authors.lastname: Lepe-Soltero
authors.affiliation: Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México. cei.abreu@cinvestav.mx.
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D015203:Reproducibility of Results; D060388:Support Vector Machine; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Biological context; Gene expression profiles; Support Vector Machine; microRNA perturbation experiments; microRNA target prediction