CLIPdb

About CLIPdb Module

The CLIPdb module provides various annotations for the RNA-binding proteins, including RNA recognition domains, gene ontology, sequence motifs, and structural preferences. All the binding sites for the query RNA binding protein and expression level for the target genes are also included.



References:
1. 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.
2. 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.
3. Flybase: Drysdale R; FlyBase Consortium. FlyBase : a database for the Drosophila research community. Methods Mol Biol. 2008;420:45-59.
4. 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.
5. 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.
6. 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.
7. Gene Ontologies: Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-29.
8. Pfam (domain): El-Gebali S, Mistry J, Bateman A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427-D432.
9. MEME: Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36.
11. Weblogo: Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188-1190.
12. RNApromo: Rabani M, Kertesz M, Segal E. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A. 2008;105(39):14885-14890.
13. RNAcontext: Kazan H, Ray D, Chan ET, Hughes TR, Morris Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol. 2010;6(7):e1000832.
15. CircInteractome circRNA binding: Dudekula DB, Panda AC, Grammatikakis I, De S, Abdelmohsen K, Gorospe M. CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2016;13(1):34-42.