RBP Binding Sites

About RBP Binding Sites Module

The RBP Binding Sites module provides annotations and functions about RNA-binding sites of the target gene with different CLIP-seq technologies and corresponding peak calling methods using table and network view, including genomic location, expression pattern of the RNA, and interaction network between RNA and RBPs.
Also, We provide the overall binding records of RBP on specific RNA precursor of each 20nt bin, which is called RBP binding hotspots.

1. Piranha: Uren PJ, Bahrami-Samani E, Burns SC, et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics. 2012;28(23):3013-3020.
2. PARalyzer (PAR-CLIP): Corcoran DL, Georgiev S, Mukherjee N, et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 2011;12(8):R79.
3. MiClip (PAR-CLIP): Wang T, Chen B, Kim M, Xie Y, Xiao G. A model-based approach to identify binding sites in CLIP-Seq data. PLoS One. 2014;9(4):e93248.
4. CIMS (HITS-CLIP): Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc. 2014;9(2):263-293.
5. CTK (HITS-CLIP): Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C. CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics. 2017;33(4):566-567.
6. Clipper (HITS-CLIP): Lovci MT, Ghanem D, Marr H, et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013;20(12):1434-1442.
7. CITS (iCLIP): Weyn-Vanhentenryck SM, Mele A, Yan Q, et al. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 2014;6(6):1139-1152.
8. PureCLIP (iCLIP): Krakau S, Richard H, Marsico A. PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. Genome Biol. 2017;18(1):240. Published 2017 Dec 28.
9. ENCODE eCLIP: Van Nostrand EL, Pratt GA, Yee BA, et al. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biol. 2020;21(1):90.
10.PIP-seq: Silverman IM, Li F, Alexander A, et al. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol. 2014;15(1):R3.
11. GENCODE annotations: Harrow J, Frankish A, Gonzalez JM, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22(9):1760-1774.
12. ZFIN: Howe DG, Ramachandran S, Bradford YM, et al. The Zebrafish Information Network: major gene page and home page updates. Nucleic Acids Res. 2021;49(D1):D1058-D1064.
13. Flybase: Drysdale R; FlyBase Consortium. FlyBase: a database for the Drosophila research community. Methods Mol Biol. 2008;420:45-59.
14. WormBase: Harris TW, Antoshechkin I, Bieri T, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010;38(Database issue):D463-D467.
15. TAIR: Lamesch P, Berardini TZ, Li D, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(Database issue):D1202-D1210.
16. SGD: Weng S, Dong Q, Balakrishnan R, et al. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003;31(1):216-218.
17. PhastCons: Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034-1050.
18. PhastCons (arabidopsis): Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell. 2012;24(11):4346-4359.
19. Phylop: Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20(1):110-121.