Investigation of RNA‐RNA Interactions Using the RISE Database. Issue 1 (8th November 2018)

• Record Type: Journal Article
• Authors: Ju, Yanyan; Gong, Jing; Yang, Yucheng T.; Zhang, Qiangfeng Cliff
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 64:Issue 1(2018)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2018-11-08
• Subjects: interaction -- RISE -- RNA -- RNA‐RNA -- RNA structure -- sequencing experiments; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.58
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: RNA‐RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome‐wide manner remained challenging until the recent development of several sequencing‐based technologies. However, RRIs generated from large‐scale studies had not been systematically collected and analyzed before. This article introduces RISE, a database of the RNA Interactome from Sequencing Experiments. RISE provides a comprehensive collection of RRIs in human, mouse, and yeast, derived from transcriptome‐wide sequencing experiments, as well as targeted sequencing studies and other public databases/datasets. To facilitate better understanding of the biological roles of these RRIs, RISE also offers rich functional annotations involving RNAs, and an interactive interface to explore the analysis results. Here, we provide a brief description of the RISE website and a step‐by‐step protocol for using RISE to study RRIs. © 2018 by John Wiley & Sons, Inc.