Finding association rules of cis-regulatory elements involved in alternative splicing

Proceedings of the Annual Southeast Conference

Volumn 2007, Issue , 2007, Pages 232-237

  Jihye, Kim ^a   Sihui, Zhao ^a   Heber, Steffen ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Alternative splicing; Association rule mining; Sequence motif; Splicing regulatory elements

Indexed keywords

ALTERNATIVE SPLICING; ASSOCIATION RULE MINING; SEQUENCE MOTIF; SPLICING REGULATORY ELEMENTS;

COMPUTATIONAL METHODS; GENES; LOGIC PROGRAMMING; MICROARRAYS; RNA; TISSUE;

PROTEINS;

EID: 34248393544     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1233341.1233383     Document Type: Conference Paper

References (25)

1. Brudno, M., et al., Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res, 2001. 29(11): p. 2338-48.
2. Caceres, J.F. and A.R. Kornblihtt, Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet, 2002. 18(4): p. 186-93.
3. Cheung, D. A Fast Distributed Algorithm for Mining Association Rules, in Proc, 4th lnt'1 Conference Parallel and Distributed Information Systems. 1996. Los Alamitos, Calif: IEEE Computer Soc. Press.
4. Fairbrother, W.G., et al., Predictive identification of exonic splicing enhancers in human genes. Science, 2002. 297(5583): p. 1007-13.
5. Faustino, N.A. and T.A. Cooper, Pre-mRNA splicing and human disease. Genes Dev, 2003. 17(4): p. 419-37.
6. Garcia-Blanco, M.A., A.P. Baraniak, and E.L. Lasda, Alternative splicing in disease and therapy. Nat Biotechnol, 2004. 22(5): p. 535-46.
7. Han, E.H.K., G.; and Kumar, V. Scalable parallel data mining for association rules. in " In ACM SIGMOD Conference Management of Data. 1997.
8. J. S. Park, M.-S.C.a.P.S.Y. An effective Hash-Based Algorithm for Mining Association Rules. in Proc. of the ACM SIGMOD Int'l Conference on Management of Data. 1995. San Jose, CA.
9. Ladd, A.N. and T.A. Cooper, Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol, 2002. 3(11): p. reviews0008.
10. Pan, Q., et al., Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell, 2004. 16(6): p. 929-41.
11. R. Agrawal, J.C.S., Parallel Mining of Association Rules. IEEE Transactions on Knowledge and Data Engineering, 1996. 8(6).
12. R. Agrawal, R.S. Fast Algorithms for Mining Association Rules. in Proc. of the 20th Int'l Conference on Very Large Databases. 1994. Santiago, Chile.
13. Rice, P., I. Longden, and A. Bleasby, EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet, 2000. 16(6): p. 276-7.
14. Shai, O., et al., Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 2006. 22(5): p. 606-13.
15. Yeo, G., et al., Variation in alternative splicing across human tissues. Genome Biol, 2004. 5(10): p. R74.
16. Zaki, M.J. Parallel Data Mining for Association Rules on Shared-Memory Multi-Processors. in Proc. Supercomputing '96. 1996. Los Alamitos, Calif: IEEE Computer Soc. Press.
17. Zhang, X.H., C.S. Leslie, and L.A. Chasin, Dichotomous splicing signals in exon flanks. Genome Res, 2005. 15(6): p. 768-79.
18. Kent, W.J., BLAT-the BLAST-like alignment tool. Genome Res, 2002. 12(4): p. 656-64.
19. Famulok, M.; Szostak, J. W., Selection of Functional RNA and DNA Molecules from Randomized Sequences. Nucleic Acids and Molecular Biology, Vol 7, F. Eckstein, D. M. J. Lilley, Eds., Springer Verlag, Berlin, 1993, pp. 271.
20. Grabowski, Paula, Alternative Splicing in Parallel, Nature Biotech, 2000. 20, 346-347.
21. Akerman, Martin; Mandel-Gutfreund Yael, Alternative Splicing regulation at tandem 3' splice sites, NAR, 2006, 34(1): p. 23-31.
22. R Development Core Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.
23. Zheng, Zhi Ming, Huynen, Martijn, Baker, Carl C.: A pirimidine-rich exonic splicing suppressor binds multiple RNA splicing factors and inhibits splicesome assembly. PNAS, 1998. 95(24).
24. Agresti, Alan, Categorical data analysis (second edition). 2002. New York: Wiley.
25. Stamm, S., J. Zhu, K. Nakai, P. Stoilov, O. Stoss, M.Q.Zhang, An alternative exon database (AEDB) and its statistical analysis. DNA and Cell Biol.2000. 19:739-756