Format

Send to

Choose Destination
BMC Genomics. 2015 Feb 5;16:51. doi: 10.1186/s12864-015-1273-2.

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

Author information

1
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. yang.thomas.yucheng@gmail.com.
2
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. dichao83@gmail.com.
3
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. hbq13@mails.tsinghua.edu.cn.
4
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. meifeng_zhou@163.com.
5
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. liuyifang3000@gmail.com.
6
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. crystal__357@163.com.
7
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. liyang01133@gmail.com.
8
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. junpeiumetsu@gmail.com.
9
Department of Biological Information, Tokyo Institute of Technology, Tokyo, 152-8850, Japan. junpeiumetsu@gmail.com.
10
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. zhilu@tsinghua.edu.cn.

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.

PMID:
25652745
PMCID:
PMC4326514
DOI:
10.1186/s12864-015-1273-2
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center