A Statistical Method for Finding Transcription Factor Binding Sites

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, ISMB 2000

Volumn , Issue , 2000, Pages 344-354

  Sinha, Saurabh ^a   Tompa, Martin ^a  

^a University of Washington ^*  (United States)

Author keywords

binding site; motif; promoter; sequence analysis; spacer; transcription factor; z score

Indexed keywords

ARTIFICIAL INTELLIGENCE; DNA SEQUENCES; MAXIMUM PRINCIPLE; STATISTICAL METHODS; TRANSCRIPTION; TRANSCRIPTION FACTORS;

BINDING-SITES; DNA BINDING SITE; GENES EXPRESSION; MOTIF; PROMOTER; SEQUENCE ANALYSIS; SPACER; SUB-PROBLEMS; TRANSCRIPTION FACTOR BINDING SITES; Z-SCORES;

BINDING SITES;

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; DNA SEQUENCE; GENETICS; HUMAN; METHODOLOGY; PROTEIN BINDING; STATISTICS;

ALGORITHMS; ANIMALS; BINDING SITES; DNA-BINDING PROTEINS; HUMANS; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA; STATISTICS; TRANSCRIPTION FACTORS;

EID: 0034564539     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (33)

1. Bailey, T. L., and Elkan, C. 1995. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21 (1-2) :51-80.
2. Blaiseau, P.-L.; Isnard, A.-D.; Surdin-Kerjan, Y.; and Thomas, D. 1997. Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Molecular and Cellular Biology 17 (7) :3640-3648.
3. Brāzma, A.; Jonassen, I.; Vilo, J.; and Ukkonen, E. 1998. Predicting gene regulatory elements in silico on a genomic scale. Genome Research 15:1202-1215.
4. Chu, S.; DeRisi, J.; Eisen, M.; Mulholland, J.; Botstein, D.; Brown, P. O.; and Herskowitz, I. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705.
5. DeRisi, J. L.; Iyer, V. R.; and Brown, P. 0. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686.
6. Feller, W. 1993. An Introduction To Probability Theory And Its Applications, volume 1. Wiley Easter Limited, third edition.
7. Fraenkel, Y. M.; Mandel, Y.; Friedberg, D.; and Margalit, H. 1995. Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Computer Applications in the Biosciences 11 (4) :379-387.
8. Galas, D. J.; Eggert, M.; and Waterman, M. S. 1985. Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli. Journal of Molecular Biology 186 (1) :117-128.
9. Guibas, L. J., and Odlyzko, A. M. 1981. String overlaps, pattern matching, and nontransitive games. Journal of Combinatorial Theory, Series A 30:183-208.
10. Hertz, G. Z., and Stormo, G. D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 (7/8) :563-577.
11. Jones, E. W.; Pringle, J. R.; and Broach, J. R., eds. 1992. The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Press.
12. Kleffe, J., and Borodovsky, M. 1992. First and second moment of counts of words in random texts generated by Markov chains. Computer Applications in the Biosciences 8 (5) :433-441.
13. Lawrence, C. E., and Reilly, A. A. 1990. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function, and Genetics 7:41-51.
14. Lawrence, C. E.; Altschul, S. F.; Boguski, M. S.; Liu, J. S.; Neuwald, A. F.; and Wootton, J. C. 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262:208-214.
15. Leung, M.-Y.; Marsh, G. M.; and Speed, T. P. 1996. Over- and underrepresentation of short DNA words in herpesvirus genomes. Journal of Computational Biology 3 (3) :345-360.
16. Mai, B., and Breeden, L. 1997. Xbp1, a stressinduced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbpl family. Molecular and Cellular Biology 17 (11) :6491-6501.
17. 1-specific transcription. Genes & Development 11:1277-1288.
18. Nicodème, P.; Salvy, B.; and Flajolet, P. 1999. Motif statistics. Technical Report RR-3606, IN-RIA Rocquencourt.
19. Nurrish, S. J., and Treisman, R. 1995. DNA binding specificity determinants in MADS-box transcription factors. Molecular and Cellular Biology 15:4076-4085.
20. Oshima, Y.; Nobuo, O.; and Harashima, S. 1996. Regulation of phosphatase synthesis in Saccharomyces cerevisiae - a review. Gene 179:171-177.
21. Régnier, M. 1998. A unified approach to word statistics. In RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, 207-213.
22. Rigoutsos, I., and Floratos, A. 1998. Motif discovery without alignment or enumeration. In RE-COMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, 221-227.
23. Rocke, E., and Tompa, M. 1998. An algorithm for finding novel gapped motifs in DNA sequences. In RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, 228-233.
24. Roth, F. P.; Hughes, J. D.; Estep, P. W.; and Church, G. M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16:939-945.
25. Salzberg, S. L.; Delcher, A. L.; Kasif, S.; and Owen, W. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Research 26 (2) :544-548.
26. Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; Iyer, V. R.; Anders, K.; Eisen, M. B.; Brown, P. O.; Botstein, D.; and Futcher, B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9:3273-3297.
27. Staden, R. 1989. Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in the Biosciences 5 (4) :293-298.
28. Tavazoie, S.; Hughes, J. D.; Campbell, M. J.; Cho, R. J.; and Church, G. M. 1999. Systematic determination of genetic network architecture. Nature Genetics 22:281-285.
29. Tompa, M. 1999. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 262-271. Heidelberg, Germany: AAAI Press.
30. van Helden, J.; André, B.; and Collado-Vides, J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 281 (5) :827-842.
31. Wemmie, J. A.; Szczypka, M. S.; Thiele, D. J.; and Moye-Rowley, W. S. 1994. Cadmium tolerance mediated by the yeast AP-1 protein requires the presence of an ATP-binding cassette transporterencoding gene, YCS1. Journal of Biological Chemistry 269 (51) :32592-32597.
32. Wingender, E.; Dietze, P.; Karas, H.; and Knüppel, R. 1996. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 24 (1) :238-241. http://transfac.gbf-braunschweig.de/TRANSFAC/
33. Zhu, J., and Zhang, M. Q. 1999. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15 (7/8) :563-577. http://cgsigma.cshl.org/jian/