Computational detection of transcription factor binding sites through differential rnyi entropy

IEEE Transactions on Information Theory

Volumn 56, Issue 2, 2010, Pages 734-741

  Maynou, Joan ^a   Gallardo Chacón, Joan Josep ^a   Vallverdú, Montserrat ^a   Caminal, Pere ^a   Perera, Alexandre ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

Binding sites; Gene regulation; Motif detection; R nyi entropy; Sequence analysis; Transcription factor

Indexed keywords

BINDING PROCESS; BINDING SEQUENCE; CANDIDATE SEQUENCES; COMPUTATIONAL APPROACH; COMPUTATIONAL DETECTION; DETECTION ALGORITHM; EXPECTATION MAXIMIZATION; GENE REGULATION; GENE REGULATIONS; MOTIF DISCOVERY; PARAMETRIC UNCERTAINTIES; PROTEIN SYNTHESIS; RECEIVER OPERATING CHARACTERISTIC CURVES; REGULATORY SEQUENCES; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SPECIFIC SEQUENCES; TRANSCRIPTION FACTOR BINDING SITES;

BINDING ENERGY; BIOCHEMISTRY; COMPUTATIONAL EFFICIENCY; ENTROPY; LAWS AND LEGISLATION; SIGNAL DETECTION; TRANSCRIPTION; TRANSCRIPTION FACTORS; UNCERTAINTY ANALYSIS;

BINDING SITES;

EID: 77649311698     PISSN: 00189448     EISSN: None     Source Type: Journal    
DOI: 10.1109/TIT.2009.2037038     Document Type: Article

References (31)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed. Garland:, 2002 [Online]. Available: http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09- 20n&path=ASIN/0815332181
2. J. D. WATSON and F. H. CRICK, "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid," Nature, vol. 171, no. 4356, pp. 737-738, Apr. 1953.
3. R. Mutihac, A. Cicuttin, and R. Mutihac, "Entropic approach to information coding in dna molecules," Mater. Sci. & Eng. C, vol. 18, no. 1-2, pp. 51-60, 2001.
4. D. T. Holloway, M. Kon, and C. DeLisi, "Classifying transcription factor targets and discovering relevant biological features," Biol. Direct. vol. 3, p. 22, 2008 [Online]. Available: http://dx.doi.org/10.1186/ 1745-6150-3-22
5. D. Latchman, Principles of Medical Biology. Greenwich, CT: JAI Press, 1996, vol. 5.
6. D. Latchman, Eukaryotic Transcription Factors, 5th ed. San Diego, CA: Academic, 2007.
7. A. G. Robert and B. R. Frieden, "Information theory in living systems, methods, applications and challenges," Bull. Math. Biol., vol. 69, pp. 635-657, 2007.
8. T. D. Schneider and R. M. Stephens, "Sequence logos: A new way to display consensus sequences," J. Mol. Biol., vol. 18, pp. 6097-6100, 1990.
9. T. D. Schneider, "Information content of individual genetic sequences," J. Theor. Biol. vol. 189, no. 4, pp. 427-441, Dec. 1997 [Online]. Available: http://dx.doi.org/10.1006/jtbi.1997.0540, [Online]. Available:
10. G. D. Stormo, "Dna binding sites: Representation and discovery," Bioinformatics, vol. 16, no. 1, pp. 16-23, Jan. 2000.
11. G. Sandve and F. Drablos, "A survey of motif discovery methods in a integrated framework," Biol. Direct., vol. 1, no. 11, 2006.
12. W. W. Wasserman and A. Sandelin, "Applied bioinformatics for the identification of regulatory elements," Nat. Rev. Genet. vol. 5, no. 4, pp. 276-287, Apr. 2004 [Online]. Available: http://dx.doi.org/10.1038/ nrg1315
13. X. S. Liu, D. L. Brutlag, and J. S. Liu, "An algorithm for finding proteindna binding sites with applications to chromatin-immunoprecipitation microarray experiments," Nat. Biotechnol. vol. 20, no. 8, pp. 835-839, Aug. 2002 [Online]. Available: http://dx.doi.org/10.1038/nbt717
14. T. Bailey and C. Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers," in Proc. 2nd Int. Conf. Intelligent Systems for Molecular Biology, Aug. 1994, pp. 28-36.
15. G. Pavesi, G. Mauri, and G. Pesole, "In silico representation and discovery of transcription factor binding sites," Briefings in Bioinform., vol. 5, no. 3, pp. 217-236, Sept. 2004.
16. T. Bailey and C. Elkan, "The value of prior knowledge in discovering motifs with meme," in Proc. Int Conf, Intelligent Systems for Molecular Biology, 1995, vol. 3, pp. 21-29.
17. T. Bailey and M. Gribskov, "Combining evidence using p-values: Application to sequence homoly searches," Bioinformatics, vol. 14, pp. 48-54, 1998.
18. A. Perera, M. Vallverdu, F. Claria, J. M. Soria, and P. Caminal, "Dna binding site characterization by means of Rényi entropy measures on nucleotide transitions," IEEE Trans Nanobiosc. vol. 7, no. 2, pp. 133-141, June 2008 [Online]. Available: http://dx.doi.org/10.1109/ TNB.2008.2000744
19. A. Krishnamachari, V. M. Mandal, and Karmeshu, "Study of dna binding sites using rényi parametric entropy measure," J. Theor. Biol., vol. 227, pp. 429-436, 2004.
20. C. Shannon, "A mathematical theroy of communication," Bell Syst. Tech. J., vol. 27, pp. 379-423, 623-656, Jul. and Oct. 1948.
21. A. Rényi, "On measures of entropy and information," in Proc. 4th Berkeley Symp. Mathematics, Statistics and Probability, Berkeley, CA, 1961, pp. 547-561.
22. M. Primig, H. Winkler, and G. Ammerer, "The dna binding and oligomerization domain of MCM1 is sufficient for its interaction with other regulatory proteins," EMBO J., vol. 10, no. 13, pp. 4209-4218, Dec. 1991.
23. B. Balasubramanian, C. V. Lowry, and R. S. Zitomer, "The rox1 repressor of the saccharomyces cerevisiae hypoxic genes is a specific dna-binding protein with a high-mobility-group motif," Mol. Cell Biol., vol. 13, no. 10, pp. 6071-6078, Oct. 1993.
24. J. J. M. T. Linde and H. Y. Steensma, "A microarray-assisted screen for potential HAP1 and ROX1 target genes in Saccharomyces cerevisiae," Yeast vol. 19, no. 10, pp. 825-840, July 2002 [Online]. Available: http://dx.doi.org/10.1002/yea.879
25. E. Wingender, X. Chen, R. Hehl, H. Karas, I. Liebich, V. Matys, T. Meinhardt, M. Prüss, I. Reuter, and F. Schacherer, "TRANSFAC: An integrated system for gene expression regulation," Nucleic Acids Res., vol. 28, no. 1, pp. 316-319, Jan. 2000.
26. R Development Core Team, R Foundation for Statistical Computing, "R: A Language and Environment for Statistical Computing," Vienna, Austria, 2008, ISBN 3-900051-07-0 [Online]. Available: http://www.R-project.org
27. R. C. Edgar, "MUSCLE: Multiple sequence alignment with high accuracy and high throughput," Nucleic Acids Res. vol. 32, no. 5, pp. 1792-1797, 2004 [Online]. Available: http://dx.doi.org/10.1093/nar/gkh340
28. B. Morgenstern, S. Goel1, A. Sczyrba, and A. Dress, "AltAVisT: Comparing alternative multiple sequence alignments," Bioinf. Applic. Note, vol. 19, no. 3, pp. 425-426, 2003.
29. T. D. Schneider, G. Stormo, L. Gold, and A. Ehrenfeuch, "The information content of binding sites on nucleotide sequences," J. Mol. Biol., vol. 188, pp. 415-431, Nov. 1986.
30. G. G. Thakurta, "Computational identification of transcriptional regulatory elements in dna sequence," Nucleic Acids Res., vol. 34, pp. 3585-3598, 2006.
31. T. Fawcett, "An introduction to roc analysis," Pattern Recognition Letters, no. 27, pp. 861-874, 2006.