title: Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.
abstract: BACKGROUND
  The pax2/5/8 genes belonging to the PAX family of transcription factors are key developmental regulators that are involved in the patterning of various embryonic tissues. More particularly, their function in inner ear specification has been widely described. However, little is known about the direct downstream targets and, so far, no global approaches have been performed to identify these target genes in this particular tissue.
  
  
  RESULTS
  Here we present an original bioinformatics pipeline composed of comparative genomics, database querying and text mining tools, which is designed to rapidly and specifically discover PAX2/5/8 direct downstream targets involved in inner ear development. We provide evidence supported by experimental validation in medaka fish that brain 2 (POU domain, class 3, transcription factor 2), claudin-7, secretory pathway component sec31-like and meteorin-like precursor are novel direct downstream targets of PAX2/5/8.
  
  
  CONCLUSIONS
  This study illustrates the power of extensive mining of public data repositories using bioinformatics methods to provide answers for a specific biological question. It furthermore demonstrates how the usage of such a combinatorial approach is advantageous for the biologist in terms of experimentation time and costs.
authors.affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany.
authors.forename: Mirana
authors.initials: M
authors.lastname: Ramialison
authors.forename: Baubak
authors.initials: B
authors.lastname: Bajoghli
authors.forename: Narges
authors.initials: N
authors.lastname: Aghaallaei
authors.forename: Laurence
authors.initials: L
authors.lastname: Ettwiller
authors.forename: Sylvain
authors.initials: S
authors.lastname: Gaudan
authors.forename: Beate
authors.initials: B
authors.lastname: Wittbrodt
authors.forename: Thomas
authors.initials: T
authors.lastname: Czerny
authors.forename: Joachim
authors.initials: J
authors.lastname: Wittbrodt
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D007758:Ear, Inner / Q000196:embryology / Q000378:metabolism*; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism; D005399:Fishes / Q000378:metabolism; D023281:Genomics; D006801:Humans; D051762:PAX2 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D051757:PAX5 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D051761:Paired Box Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D029941:Fish Proteins; D051762:PAX2 Transcription Factor; D051757:PAX5 Transcription Factor; D051761:Paired Box Transcription Factors