Searching for statistically significant regulatory modules

Bioinformatics

Volumn 19, Issue SUPPL. 2, 2003, Pages

  Bailey, Timothy L ^a   Noble, William Stafford ^b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; TRANSCRIPTION FACTOR;

ALGORITHM; BINDING SITE; CONFERENCE PAPER; DNA SEQUENCE; GENE CLUSTER; GENE EXPRESSION REGULATION; GENETIC MODEL; GENETIC TRANSCRIPTION; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN DNA INTERACTION; SEQUENCE ALIGNMENT; SIMULATION;

EID: 4043156577     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1054     Document Type: Conference Paper

References (30)

1. Bailey, T.L. (2003) Details of MCAST statistics, Technical Report IMB TR0001, Institute for Molecular Bioscience, University of Queensland, http://www.maths.uq.edu.au/~tlb.
2. Bailey, T.L. and Elkan, C.P. (1994) Fitting a mixture model by expectation-maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 28-36.
3. Bailey, T.L. and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
4. Bailey, T.L. and Gribskov, M. (2002) Estimating and evalutating the statistics of gapped local-alignment scores. J. Comp. Biol., 9, 573-593.
5. Benson, G. Tandem repeats finder: a program to analyze dna sequences. Nucleic Acids Res., 27, 573-580.
6. Berman, B.P., Nibu, Y., Pfeifer, B.D., Tomancak, R, Celniker, S.E., Levine, M., Rubin, G.M. and Eisen, M.B. (2002) 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.
7. Bucher, P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
8. Crowley, E.M., Roeder, K. and Bina, M. (1997) A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol., 268, 8-14.
9. Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc., 39(1), 1-38.
10. Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. (1998) Biological Sequence Analysis. Cambridge UP.
11. Frech, K., Danescu-Mayer, J. and Werner, T. (1997) A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J. Mol. Biol., 270, 674-687.
12. Frith, M.C., Hansen, U. and Weng, Z. (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 17(10), 878-889.
13. Frith, M.C., Spouge, J.L., Hansen, U. and Weng, Z. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res., 30(14), 3214-3224.
14. Gribskov, M. and Robinson, N.L. (1996) The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comp. & Chem., 20, 25-33.
15. Grundy, W.N., Bailey, T.L., Elkan, C.P. and Baker, M.E. (1997) Meta-MEME: Motif-based hidden Markov models of protein families. Comp. Appl. Biosci., 13(4), 397-406.
16. Klingenhoff, A., Frech, K., Quandt, K. and Werner, T. (1999) Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics, 15, 180-186.
17. Kondrakhin, Y.V., Kel, A.E., Kolchanov, N.A., Romashchenko, A.G. and Milanesi, L. (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comp. Appl. Biosci., 11, 477-488.
18. Krivan, W. and Wasserman, W. (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res., 11, 1559-1566.
19. Krogh, A., Brown, M., Mian, I., Sjolander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
20. Levy, S. and Hannenhalli, S. (2002) Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome, 13, 510-514.
21. Markstein, M., Markstein, P., Markstein, V. and Levine, M.S. (2002) Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl Acad. Sci USA, 99(2), 763-768.
22. Mouse Genome Sequencing Consortium, (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
23. Pavlidis, P., Furey, T.S., Liberto, M., Haussler, D. and Grundy, W.N. (2001) Promoter region-based classification of genes. In Proceedings of the Pacific Symposium on Biocomputing. pp. 151-163.
24. Prestridge, D. (1995) Predicting Pol II promoter sequences using transcription factor binding sites. J. Mol. Biol., 249, 923-932.
25. Ptashne, M. and Gann, A. (2002) Genes and Signals. Cold Spring Harbor Laboratory Press.
26. Schaffer, A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., Koonin, E.V. and Altschul, S.F. (2001) Improving the accuracy of psi-blast protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
27. Viterbi, A.J. (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Info. Theory, IT-13, 260-269.
28. Wasserman, W.W. and Fickett, J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
29. Waterman, M. and Eggert, M. (1987) A new algorithm for best subsequence alignments with application to tRNA-tRNA comparisons. J. Mol. Biol., 197, 723-725.
30. Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I. and Schacherer, F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.