title: doRiNA: a database of RNA interactions in post-transcriptional regulation.
abstract: In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.
authors.affiliation: Bioinformatics in Quantitative Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
authors.forename: Gerd
authors.initials: G
authors.lastname: Anders
authors.forename: Sebastian D
authors.initials: SD
authors.lastname: Mackowiak
authors.forename: Marvin
authors.initials: M
authors.lastname: Jens
authors.forename: Jonas
authors.initials: J
authors.lastname: Maaskola
authors.forename: Andreas
authors.initials: A
authors.lastname: Kuntzagk
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Rajewsky
authors.forename: Markus
authors.initials: M
authors.lastname: Landthaler
authors.forename: Christoph
authors.initials: C
authors.lastname: Dieterich
mesh_terms: D000818:Animals; D001665:Binding Sites; D050756:Cyclin-Dependent Kinase Inhibitor Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*
chemical_list: D050756:Cyclin-Dependent Kinase Inhibitor Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
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