Prediction of mRNA polyadenylation sites by support vector machine

Bioinformatics

Volumn 22, Issue 19, 2006, Pages 2320-2325

  Cheng, Yiming ^a,b   Miura, Robert M ^a   Tian, Bin ^a  

^a NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; MESSENGER RNA; URACIL;

ARTICLE; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; HUMAN; HUMAN CELL; MACHINE; POLYADENYLATION; PREDICTION; PRIORITY JOURNAL; RNA PROCESSING; RNA SEQUENCE; RNA VECTOR; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

EUKARYOTA;

EID: 33749997848     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl394     Document Type: Article

References (28)

1. Bennett,C.L. et al. (2001) A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA→AAUGAA) leads to the IPEX syndrome. Immunogenetics, 53, 435-439.
2. Buratowski,S. (2005) Connections between mRNA 3′ end processing and transcription termination. Curr. Opin. Cell Biol., 17, 257-261.
3. Burges,C.J.C. and Smola,A.J. (1998) Advances in Kernel Methods-Support Vector Learning. MIT Press, Cambridge, MA.
4. Colgan,D.F. and Manley,J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes. Dev., 11, 2755-2766.
5. Cortes,C. and Vapnik,V. (1995) Support-vector networks, Machine Learning, 20, 273-297.
6. Frischmeyer,P.A. et al. (2002) An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science, 295, 2258-2261.
7. Gehring,N.H. et al. (2001) Increased efficiency of mRNA 3′ end formation: A new genetic mechanism contributing to hereditary thrombophilia. Nat. Genet, 28, 389-392.
8. Graber,J.H. (2003) Variations in yeast 3′-processing cis-elements correlate with transcript stability. Trends. Genet, 19, 473-476.
9. Graber,J.H. et al. (1999) In silico detection of control signals: MRNA 3′-end-processing sequences in diverse species. Proc. Natl Acad. Sci. USA, 96, 14055-14060.
10. Graber,J.H. et al. (2002) Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites. Nucleic Acids Res., 30, 1851-1858.
11. Hajarnavis,A. et al. (2004) A probabilistic model of 3′ end formation in Caenorhabditis elegans. Nucleic Acids Res., 32, 3392-3399.
12. Hu,J. et al. (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA, 11, 1485-1493.
13. Legendre,M. and Gautheret,D. (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics, 4, 7.
14. Perez Canadillas,J.M. and Varani,G. (2003) Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein. EMBO. J, 22, 2821-2830.
15. Proudfoot,N. (2004) New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol., 16, 272-278.
16. Pruitt,K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
17. Salamov,A.A. and Solovyev,V.V. (1997) Recognition of 30-processing sites of human mRNA precursors. Comput. Appl. Biosci., 13, 23-28.
18. Tabaska,J.E. and Zhang,M.Q. (1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231, 77-86.
19. Tian,B. et al. (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res., 33, 201-212.
20. Venkataraman,K. et al. (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes. Dev., 19, 1315-1327.
21. Yan,J. and Marr,T.G. (2005) Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome. Res., 15, 369-375.
22. Yeo,G. et al. (2004) Variation in alternative splicing across human tissues. Genome Biol., 5, R74.
23. Zarudnaya,M.I. et al. (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures. Nucleic Acids Res., 31, 1375-1386.
24. Zhang,H. et al. (2005a) PolyA_DB: A database for mammalian mRNA polyadenylation. Nucleic Acids Res., 33, D116-D120.
25. Zhang,H. et al. (2005b) Biased alternative polyadenylation in human tissues. Genome Biol., 6, R100.
26. Zhang,M.Q. (2000) Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform., 1, 331-342.
27. Zhang,X.H. et al. (2003) Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome. Res., 13, 2637-2650.
28. Zhao,J. et al. (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev, 63, 405-445.