CLIPdb: a CLIP-seq database for protein-RNA interactions

BMC Genomics. 2015 Feb 5;16(1):51. doi: 10.1186/s12864-015-1273-2.

Abstract

Background: 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. 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.

Description: 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. We consistently annotated the CLIP-seq data sets and RBPs, and developed a user-friendly interface for rapid navigation of the CLIP-seq data. 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. The high-resolution binding sites of the RBPs can be visualized on the whole-genome scale using a browser. 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.

Conclusion: 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. With maintained up-to-date data sets and improved functionality, CLIPdb ( http://clipdb.ncrnalab.org ) will be a valuable resource for improving the understanding of post-transcriptional regulatory networks.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic
  • Gene Expression Regulation
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mice
  • Protein Interaction Maps / genetics*
  • Proteins / genetics*
  • RNA, Long Noncoding / genetics
  • RNA, Messenger / genetics*
  • RNA-Binding Proteins / genetics*
  • Sequence Analysis, RNA
  • Software*
  • Transcriptome / genetics

Substances

  • Proteins
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA-Binding Proteins