RBPmap: A web server for mapping binding sites of RNA-binding proteins

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Paz, Inbal ^a   Kosti, Idit ^a   Ares Jr , Manuel ^b   Cline, Melissa ^c   Mandel Gutfreund, Yael ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; DROSOPHILA MELANOGASTER; FALSE NEGATIVE RESULT; HUMAN; MEASUREMENT ACCURACY; MOUSE; NONHUMAN; ONLINE SYSTEM; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN MOTIF; RBPMAP; RNA BINDING; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; VALIDATION PROCESS; WEB BROWSER;

DROSOPHILA MELANOGASTER;

ALGORITHMS; ANIMALS; BINDING SITES; DROSOPHILA MELANOGASTER; HUMANS; INTERNET; MICE; NUCLEOTIDE MOTIFS; RNA; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84904820636     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku406     Document Type: Article

References (35)

1. Li,X., Kazan,H., Lipshitz,H.D. and Morris,Q.D. (2014) Finding the target sites of RNA-binding proteins. Wiley Interdiscip. Rev. RNA, 5, 111-130.
2. Ray,D., Kazan,H., Chan,E.T., Peña Castillo,L., Chaudhry,S., Talukder,S., Blencowe,B.J., Morris,Q. and Hughes,T.R. (2009) Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol., 27, 667-670.
3. Ray,D., Kazan,H., Cook,K.B., Weirauch,M.T., Najafabadi,H.S., Li,X., Gueroussov,S., Albu,M., Zheng,H., Yang,A. et al. (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature, 499, 172-177.
4. Tenenbaum,S.A., Carson,C.C., Lager,P.J. and Keene,J.D. (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. PNAS, 97, 14085-14090.
5. Keene,J.D., Komisarow,J.M. and Friedersdorf,M.B. (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protoc., 1, 302-307.
6. Ule,J., Jensen,K.B., Ruggiu,M., Mele,A., Ule,A. and Darnell,R.B. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science, 302, 1212-1215.
7. Licatalosi,D.D., Mele,A., Fak,J.J., Ule,J., Kayikci,M., Chi,S.W., Clark,T.A., Schweitzer,A.C., Blume,J.E., Wang,X. et al. (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature, 456, 464-469.
8. König,J., Zarnack,K., Rot,G., Curk,T., Kayikci,M., Zupan,B., Turner,D.J., Luscombe,N.M. and Ule,J. (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol., 17, 909-915.
9. Hafner,M., Landthaler,M., Burger,L., Khorshid,M., Hausser,J., Berninger,P., Rothballer,A., Ascano,M. Jr, Jungkamp,A.-C., Munschauer,M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141, 129-141.
10. Khorshid,M., Rodak,C. and Zavolan,M. (2011) CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res., 39, D245-D252.
11. Anders,G., Mackowiak,S.D., Jens,M., Maaskola,J., Kuntzagk,A., Rajewsky,N., Landthaler,M. and Dieterich,C. (2011) doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res., 40, D180-D186.
12. Yao,Z., Weinberg,Z. and Ruzzo,W.L. (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452.
13. Hiller,M., Pudimat,R., Busch,A. and Backofen,R. (2006) Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res., 34, e117.
14. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
15. Linhart,C., Halperin,Y. and Shamir,R. (2008) Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Res., 18, 1180-1189.
16. Georgiev,S., Boyle,A.P., Jayasurya,K., Ding,X., Mukherjee,S. and Ohler,U. (2010) Evidence-ranked motif identification. Genome Biol., 11, R19.
17. Leibovich,L., Paz,I., Yakhini,Z. and Mandel-Gutfreund,Y. (2013) DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. Nucleic Acids Res., 41, W174-W179.
18. Grillo,G., Turi,A., Licciulli,F., Mignone,F., Liuni,S., Banfi,S., Gennarino,V.A., Horner,D.S., Pavesi,G., Picardi,E. et al. (2010) UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res., 38, D75-D80.
19. Pesole,G., Liuni,S., Grillo,G., Licciulli,F., Larizza,A., Makalowski,W. and Saccone,C. (2000) UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Nucleic Acids Res., 28, 193-196.
20. Cook,K.B., Kazan,H., Zuberi,K., Morris,Q. and Hughes,T.R. (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res., 39, D301-D308.
21. Cartegni,L.,Wang,J., Zhu,Z., Zhang,M.Q. and Krainer,A.R. (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucl. Acids Res., 31, 3568-3571.
22. Huang,H.-Y., Chien,C.-H., Jen,K.-H. and Huang,H.-D. (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res., 34, W429-W434.
23. Paz,I., Akerman,M., Dror,I., Kosti,I. and Mandel-Gutfreund,Y. (2010) SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res., 38, W281-W285.
24. Akerman,M., David-Eden,H., Pinter,R.Y. and Mandel-Gutfreund,Y. (2009) A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol., 10, R30.
25. Kosti,I., Radivojac,P. andMandel-Gutfreund,Y. (2012) An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. PLoS Comput. Biol., 8, e1002603.
26. Cereda,M., Pozzoli,U., Rot,G., Juvan,P., Schweitzer,A., Clark,T. and Ule,J. (2014) RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol., 15, R20.
27. Zhang,C., Lee,K.-Y., Swanson,M.S. and Darnell,R.B. (2013) Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res., 41, 6793-6807.
28. Siepel,A., Bejerano,G., Pedersen,J.S., Hinrichs,A.S., Hou,M., Rosenbloom,K., Clawson,H., Spieth,J., Hillier,L.W., Richards,S. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
29. Kent,W.J. (2002) BLAT-The BLAST-Like Alignment Tool. Genome Res., 12, 656-664.
30. Grillo,G., Licciulli,F., Liuni,S., Sbisà,E. and Pesole,G. (2003) PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res., 31, 3608-3612.
31. Jacobs,G.H., Stockwell,P.A., Tate,W.P. and Brown,C.M. (2006) Transterm-extended search facilities and improved integration with other databases. Nucl. Acids Res., 34, D37-D40.
32. Huelga,S.C., Vu,A.Q., Arnold,J.D., Liang,T.Y., Liu,P.P., Yan,B.Y., Donohue,J.P., Shiue,L., Hoon,S., Brenner,S. et al. (2012) Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep., 1, 167-178.
33. Xue,Y., Zhou,Y.,Wu,T., Zhu,T., Ji,X., Kwon,Y.-S., Zhang,C., Yeo,G., Black,D.L., Sun,H. et al. (2009) Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol. Cell, 36, 996-1006.
34. Tollervey,J.R., Curk,T., Rogelj,B., Briese,M., Cereda,M., Kayikci,M., König,J., Hortobágyi,T., Nishimura,A.L., Z upunski,V. et al. (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat. Neurosci., 14, 452-458.
35. Corcoran,D.L., Georgiev,S., Mukherjee,N., Gottwein,E., Skalsky,R.L., Keene,J.D. and Ohler,U. (2011) PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol., 12, R79.