RBPome RBPome

An integrative resource of CLIP-seq studies

Welcome to CLIPdb

CLIPdb aims to characterize the regulatory networks between RNA binding proteins (RBPs) and various RNA transcript classes by integrating large amounts of CLIP-seq (including HITS-CLIP, PAR-CLIP and iCLIP as variantions) data sets.
CLIPdb consistently annotated the CLIP-seq data sets and RBPs, and provides a user-friendly interface for quick navigation of the CLIP-seq data. To make the binding sites directly comparable and integratable across different CLIP-seq studies, CLIPdb applied uniform computational methods to identify transcriptome-wide binding sites using raw CLIP-seq data. Users can download the RBP binding sites of their interests.
We will continue to enrich CLIPdb with more CLIP-seq data sets, and other high-throughput post-transcriptional regulatory data, including ribosome profiling data sets.
CLIPdb 2 - POSTAR is available at http://POSTAR.ncrnalab.org.

Statistics

Species Human, Mouse, Worm, Yeast
Technology HITS-CLIP, PAR-CLIP, iCLIP, gPAR-CLIP
CLIP-seq datasets 426
Number of RBPs 119
Number of cell lines 27
Total CLIP-seq reads ~8.5 billions
Summary table click

News

  • Update: 45 data sets added on August, 2016.
  • Update: 17 data sets added on July, 2016.
  • Update: 17 data sets added on April, 2015.
  • First update: 8 human HITS-CLIP data sets added on December, 2014
  • CLIPdb 1.0 release in September, 2014.

  • More>>

    Citation

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

    Yu-Cheng T. Yang*, Chao Di*, Boqin Hu*, Meifeng Zhou, Nanxi Song, Yang Li, Yifang Liu, Jumpei Umetsu, and Zhi John Lu

    BMC Genomics 16:51 (2015)

    *co-first authors

    POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.

    Hu B*, Yang YT*, Huang YM, Zhu YM and Lu ZJ

    NAR(2016)

    *co-first authors