title: CLIPdb: a CLIP-seq database for protein-RNA interactions.
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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors: 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.
authors: Yu-Cheng T
authors: YC
authors: Yang
authors: 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.
authors: Chao
authors: C
authors: Di
authors: 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.
authors: Boqin
authors: B
authors: Hu
authors: 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.
authors: Meifeng
authors: M
authors: Zhou
authors: 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.
authors: Yifang
authors: Y
authors: Liu
authors: 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.
authors: Nanxi
authors: N
authors: Song
authors: 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.
authors: Yang
authors: Y
authors: Li
authors: 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.|Department of Biological Information, Tokyo Institute of Technology, Tokyo, 152-8850, Japan. junpeiumetsu@gmail.com.
authors: Jumpei
authors: J
authors: Umetsu
authors: 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.
authors: Zhi John
authors: ZJ
authors: Lu
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D060066:Protein Interaction Maps / Q000235:genetics*; D011506:Proteins / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome / Q000235:genetics
chemical_list: D011506:Proteins; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
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