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.
| 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 |
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