title: The microRNA body map: dissecting microRNA function through integrative genomics.
abstract: While a growing body of evidence implicates regulatory miRNA modules in various aspects of human disease and development, insights into specific miRNA function remain limited. Here, we present an innovative approach to elucidate tissue-specific miRNA functions that goes beyond miRNA target prediction and expression correlation. This approach is based on a multi-level integration of corresponding miRNA and mRNA gene expression levels, miRNA target prediction, transcription factor target prediction and mechanistic models of gene network regulation. Predicted miRNA functions were either validated experimentally or compared to published data. The predicted miRNA functions are accessible in the miRNA bodymap, an interactive online compendium and mining tool of high-dimensional newly generated and published miRNA expression profiles. The miRNA bodymap enables prioritization of candidate miRNAs based on their expression pattern or functional annotation across tissue or disease subgroup. The miRNA bodymap project provides users with a single one-stop data-mining solution and has great potential to become a community resource.
authors.affiliation: Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium and Life Technologies, Foster City, CA, USA. pieter.mestdagh@ugent.be
authors.forename: Pieter
authors.initials: P
authors.lastname: Mestdagh
authors.forename: Steve
authors.initials: S
authors.lastname: Lefever
authors.forename: Filip
authors.initials: F
authors.lastname: Pattyn
authors.forename: Dana
authors.initials: D
authors.lastname: Ridzon
authors.forename: Erik
authors.initials: E
authors.lastname: Fredlund
authors.forename: Annelies
authors.initials: A
authors.lastname: Fieuw
authors.forename: Maté
authors.initials: M
authors.lastname: Ongenaert
authors.forename: Joëlle
authors.initials: J
authors.lastname: Vermeulen
authors.forename: Anne
authors.initials: A
authors.lastname: De Paepe
authors.forename: Linda
authors.initials: L
authors.lastname: Wong
authors.forename: Frank
authors.initials: F
authors.lastname: Speleman
authors.forename: Caifu
authors.initials: C
authors.lastname: Chen
authors.forename: Jo
authors.initials: J
authors.lastname: Vandesompele
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D057225:Data Mining; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000378:metabolism; D051381:Rats; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors