Logos: A modular Bayesian model for de novo motif detection

Journal of Bioinformatics and Computational Biology

Volumn 2, Issue 1, 2004, Pages 127-154

  Xing, Eric P ^a   Wu, Wei ^b   Jordan, Michael I ^c   Karp, Richard M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bayesian model; Cis regulatory system; Dirichlet prior; Hidden Markov model; Variational inference

Indexed keywords

BIOPOLYMER;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; COMPUTER ANALYSIS; DROSOPHILA; EUKARYOTE; FUNGAL GENE; GENOME; MATHEMATICAL MODEL; NONHUMAN; PROTEIN ANALYSIS; PROTEIN MOTIF; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; BAYES THEOREM; DNA; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

EUKARYOTA;

EID: 3242687409     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000508     Document Type: Article

References (27)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, Molecular Biology of the Cell, 4th Edition. Taylor and Francis (2002).
2. T. L. Bailey and C. Elkan, "Unsupervised learning of multiple motifs in biopolymers using EM," Machine Learning 21, 51-80 (1995).
3. Y. Barash, G. Elidan, N. Friedman and T. Kaplan, "Modeling dependencies in protein-DNA binding sites," In RECOMB (2003).
4. B. P. Berman, Y. Nibu, B. D. Pfeiffer, P. Tomancak, S. E. Celniker, M. Levine, G. M. Rubin and M. B. Eisen, "Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome," Proc. Natl. Acad. Sci. USA 99, 757-762 (2002).
5. H. Bussemaker, H. Li and E. Siggia, "Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis," Proc. Natl. Acad. Sci. USA 97 (2000).
6. H. J. Bussemaker, H. Li and E. D. Siggia, "Regulatory element detection using correlation with expression," Nat. Genet. 27(2), 167-171 (2001).
7. E. H. Davidson, Genomic Regulatory Systems. Academic Press (2001).
8. B. Efron, "Empirical Bayes methods for combining likelihoods (with discussion)", J. Amer. Statist. Assoc. 91, 538-565 (1996).
9. M. Eisen, "Structural properties of transcription factor-DNA interactions and the inference of sequence specificity," submitted (2003).
10. M. C. Frith, U. Hansen and Z. Weng, "Detection of cis-element clusters in higher eukaryotic DNA," Bioinform. 17, 878-889 (2001).
11. D. GuhaThakurta and G. D. Stormo, "Identifying target sites for cooperatively binding factors," Bioinform. 17, 608-621 (2001).
12. M. Gupta and J. Liu, "Discovery of conserved sequence patterns using a stochastic dictionary model," J. Amer. Statist. Assoc. 98 (2003).
13. J. V. Helden, A. Rios and J. Collado-Vides, "Discovering regulatory elements in non-coding sequences by analysis of spaced dyads," Nucleic Acids Res. 28, 1808-1818 (2000).
14. G. Z. Hertz and G. D. Stormo, "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences," Bioinform. 15, 563-577 (1999).
15. H. Huang, M. Kao, X. Zhou, J. S. Liu and W. H. Wong, "Determination of local statistical significance of patterns in Markov with application to promoter element identification," Journal of Computational Biology (in press).
16. M. I. Jordan, Z. Ghahramani, T. S. Jaakkola and L. K. Saul, "An introduction to variational methods for graphical models," in M. I. Jordan (ed.) Learning in Graphical Models. MIT Press, Cambridge (1999).
17. K. Kechris, E. van Zwet, P. Bickel and M. Eisen, "Detecting DNA regulatory motifs by incoporating position-specific base conservation," submitted (2003).
18. J. Liu, A. Neuwald and C. Lawrence, "Bayesian models for multiple local sequence alignment and Gibbs sampling strategies," J. Amer. Statist. Assoc. 90, 1156-1169 (1995).
19. X. Liu, D. Brutlag and J. Liu, "Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes," Proc. of Pac. Symp. Biocomput., pp. 127-138 (2001).
20. X. S. Liu, D. L. Brutlag and J. S. Liu, "An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments," Nat. Biotechnol. 20(8), 835-839 (2002).
21. F. P. Roth, J. D. Hughes, P. W. Estep and G. M. Church, "Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation," Nat. Biotechnol. 16(10), 939-945 (1998).
22. T. D. Schneider and R. M. Stephens, "Sequence logos: A new way to display consensus sequences," Nucl. Acids Res. 18, 6097-6100 (1990).
23. K. Sjölander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I. Mian and D. Haussler, "Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology," Computer Applications in the Biosciences 12 (1996).
24. G. D. Stormo and D. S. Fields, "Specificity, free energy and information content in protein-DNA interactions," Trends in Biochemical Sciences 23, 109-113 (1998).
25. L. Stryer, Biochemistry (4th edition). W. H. Freeman and Company (1995).
26. E. P. Xing, M. I. Jordan, R. M. Karp and S. Russell, "A hierarchical Bayesian Markovian model for motifs in biopolymer sequences," Proc. of Advances in Neural Information Processing Systems 16 (2003).
27. E. P. Xing, M. I. Jordan and S. Russell, "A generalized mean field algorithm for variational inference in exponential families," Proceedings of the 19th Annual Conference on Uncertainty in AI (2003).