CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

The stability, localization and translation rate of mRNAs are regulated by a multitude of RNAbinding 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 li...

• Type: Journal
• Year: 2011
• Where: NAR
• Authors: Mohsen Khorshid, Christoph Rodak, Mihaela Zavolan
• Keywords: Insulin Like Growth Factor, NAR 2011, Regulatory Elements, Sequence Data Sets