The "RBP" module provides various annotations for the RNA Binding Proteins, including RNA recognition domains, RBP ontology, sequence motifs and structural preferences. All the binding sites for the query RBP and expression level for the target genes are also included.
Search RNA Binding Protein Module by selecting species and entering RBP name.
We move CLIPdb here and keep updating it.
1. Piranha: Uren P.J. et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 28, 3013-20 (2012).
2. PARalyzer (PAR-CLIP): Corcoran D.L. et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 12, R79 (2011).
3. CIMS (HITS-CLIP): Moore M. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 9, 263-93 (2014).
4. CITS (iCLIP): Weyn-Vanhentenryck S.M. et al. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep 6, 1139-52 (2014).
5. ENCODE eCLIP: Van Nostrand E.L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods (2016).
6. RNAcontext: Kazan H et al. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol (2010).
7. RNApromo: Rabani M et al. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A. (2008).
8. Pfam: Finn RD et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. (2016).
9. AmiGO: Seth Carbon et al. AmiGO: online access to ontology and annotation data. Bioinformatics. (2009).