title: CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.
abstract: The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.
authors.affiliation: Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Khorshid
authors.forename: Christoph
authors.initials: C
authors.lastname: Rodak
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
mesh_terms: D000818:Animals; D001665:Binding Sites; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D012343:RNA, Transfer