SFmap: A web server for motif analysis and prediction of splicing factor binding sites

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Paz, Inbal ^a   Akerman, Martin ^b   Dror, Iris ^a   Kosti, Idit ^a   Mandel Gutfreund, Yael ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; RNA BINDING PROTEIN; SPLICING FACTOR; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; ARTICLE; BINDING SITE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DATABASE; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; ALGORITHM; HUMAN; HUMAN GENOME; METABOLISM; SEQUENCE ANALYSIS;

ALGORITHMS; ALTERNATIVE SPLICING; BINDING SITES; GENOME, HUMAN; HUMANS; INTERNET; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA; SOFTWARE; USER-COMPUTER INTERFACE;

EUKARYOTA;

EID: 77954284248     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq444     Document Type: Article

References (20)

1. Chen,M. and Manley,J.L. (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell. Biol., 10, 741-754.
2. Cooper,T.A., Wan,L. and Dreyfuss,G. (2009) RNA and disease. Cell, 136, 777-793.
3. Schwartz,S., Hall,E. and Ast,G. (2009) SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res., 37, W189-W192.
4. Wang,Z. and Burge,C.B. (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA, 14, 802-813.
5. Ladd,A.N. and Cooper,T.A. (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol., 3, reviews0008.
6. Cartegni,L., Wang,J., Zhu,Z., Zhang,M.Q. and Krainer,A.R. (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res., 31, 3568-3571.
7. Fairbrother,W.G., Yeo,G.W., Yeh,R., Goldstein,P., Mawson,M., Sharp,P.A. and Burge,C.B. (2004) RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res., 32, W187-W190.
8. Zhang,X.H., Kangsamaksin,T., Chao,M.S., Banerjee,J.K. and Chasin,L.A. (2005) Exon inclusion is dependent on predictable exonic splicing enhancers. Mol. Cell Biol., 25, 7323-7332.
9. Wang,Z., Rolish,M.E., Yeo,G., Tung,V., Mawson,M. and Burge,C.B. (2004) Systematic identification and analysis of exonic splicing silencers. Cell, 119, 831-845.
10. Goren,A., Ram,O., Amit,M., Keren,H., Lev-Maor,G., Vig,I., Pupko,T. and Ast,G. (2006) Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers. Mol. Cell, 22, 769-781.
11. Chasin,L.A. (2007) Searching for splicing motifs. Adv. Exp. Med. Biol., 623, 85-106.
12. Smith,P.J., Zhang,C., Wang,J., Chew,S.L., Zhang,M.Q. and Krainer,A.R. (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum. Mol. Genet., 15, 2490-2508.
13. 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.
14. 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.
15. Kuhn,R.M., Karolchik,D., Zweig,A.S., Wang,T., Smith,K.E., Rosenbloom,K.R., Rhead,B., Raney,B.J., Pohl,A., Pheasant,M. et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
16. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
17. Sureau,A., Gattoni,R., Dooghe,Y., Stevenin,J. and Soret,J. (2001) SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J., 20, 1785-1796.
18. Dreumont,N., Hardy,S., Behm-Ansmant,I., Kister,L., Branlant,C., Stevenin,J. and Bourgeois,C.F. (2009) Antagonistic factors control the unproductive splicing of SC35 terminal intron. Nucleic Acids Res., 38, 1353-1366.
19. Buratti,E. and Baralle,F.E. (2008) Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. Front. Biosci., 13, 867-878.
20. Gupta,Y.K., Lee,T.H., Edwards,T.A., Escalante,C.R., Kadyrova,L.Y., Wharton,R.P. and Aggarwal,A.K. (2009) Co-occupancy of two Pumilio molecules on a single hunchback NRE. RNA, 15, 1029-1035.