![]() With the development of next-generation sequencing technologies, crosslinking immunoprecipitation (CLIP)-seq technology, which includes high-throughput sequencing (HITS)-CLIP, photoactivatable ribonucleoside-enhanced (PAR)-CLIP and individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), has become a powerful tool to study the transcriptome-wide in vivo binding sites of RBPs at the single-nucleotide level. In recent years, much progress has been made in the field of ribonomics, which uses high-throughput technologies to investigate the interactions between RBPs and their target RNAs, including coding and non-coding RNAs, in a quantitative and high-resolution manner. RNA binding proteins (RBPs) play essential roles in the co-transcriptional and post-transcriptional regulation of gene expression. With maintained up-to-date data sets and improved functionality, CLIPdb ( ) will be a valuable resource for improving the understanding of post-transcriptional regulatory networks. Manually curated metadata and uniformly identified binding sites of publicly available CLIP-seq data sets will be a foundation for further integrative and comparative analyses. In addition, users can browse and download the identified binding sites of all profiled RBPs by querying genes of interest, including both protein coding genes and non-coding RNAs. The high-resolution binding sites of the RBPs can be visualized on the whole-genome scale using a browser. We applied a unified computational method to identify transcriptome-wide binding sites, making the binding sites directly comparable and the data available for integration across different CLIP-seq studies. We consistently annotated the CLIP-seq data sets and RBPs, and developed a user-friendly interface for rapid navigation of the CLIP-seq data. Here, we constructed a database, CLIPdb, to describe RBP-RNA interactions based on 395 publicly available CLIP-seq data sets for 111 RBPs from four organisms: human, mouse, worm and yeast. Large amounts of crosslinking immunoprecipitation (CLIP)-seq data (including HITS-CLIP, PAR-CLIP, and iCLIP) have been recently produced to reveal transcriptome-wide binding sites of RBPs at the single-nucleotide level. RNA-binding proteins (RBPs) play essential roles in gene expression regulation through their interactions with RNA transcripts, including coding, canonical non-coding and long non-coding RNAs.
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