title: SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins.
abstract: microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.
authors.affiliation: a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany.|b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Preusse
authors.affiliation: a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Marr
authors.affiliation: c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.
authors.forename: Sita
authors.initials: S
authors.lastname: Saunders
authors.affiliation: c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Maticzka
authors.affiliation: b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.|d Medical Faculty; Technische Universität München ; Munich , Germany.
authors.forename: Heiko
authors.initials: H
authors.lastname: Lickert
authors.affiliation: c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.|e BIOSS Center for Biological Signaling Studies; Cluster of Excellence; University of Freiburg ; Freiburg , Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.affiliation: b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.|f Technische Universität München; Center for Mathematics; Chair of Mathematical Modeling of Biological Systems ; Garching , Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Theis
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012984:Software; D064878:Web Browser
chemical_list: D035683:MicroRNAs; D016601:RNA-Binding Proteins
keywords: RNA-binding proteins; coregulation; functional similarity; microRNAs; web application.