Combining phylogenetic data with co-regulated genes to identify regulatory motifs

Bioinformatics

Volumn 19, Issue 18, 2003, Pages 2369-2380

  Wang, Ting ^a   Stormo, Gary D ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE CONTROL; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC CONSERVATION; INTERMETHOD COMPARISON; MOLECULAR PHYLOGENY; PRIORITY JOURNAL; PROTEIN FOOTPRINTING; PROTEIN MOTIF; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATISTICAL ANALYSIS;

EID: 0344906814     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg329     Document Type: Article

References (30)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
3. Bailey,T.L. and Elkan,C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 21-29.
4. Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
5. Blanchette,M., Schwikowski,B. and Tompa,M. (2002) Algorithms for phylogenetic footprinting. J. Comput. Biol., 9, 211-223.
6. Blanchette,M. and Tompa,M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739-748.
7. Buhler,J. and Tompa,M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
8. Cliften,P., Sudarsanam,P., Desikan,A., Fulton,L., Fulton,B., Majors,J., Waterston,R., Cohen,B.A. and Johnston,M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71-76.
9. Cliften,P.F., Hillier,L.W., Fulton,L., Graves,T., Miner,T., Gish,W.R., Waterston,R.H. and Johnston,M. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res., 11, 1175-1186.
10. Eskin,E. and Pevzner,P.A. (2002) Finding composite regulatory patterns in DNA sequences. Bioinformatics, 18, S354-S363.
11. Gelfand,M.S., Koonin,E.V. and Mironov,A.A. (2000) Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res., 28, 695-705.
12. GuhaThakurta,D., Palomar,L., Stormo,G.D., Tedesco,P., Johnson,T.E., Walker,D.W., Lithgow,G., Kim,S. and Link,C.D. (2002) Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res., 12, 701-712.
13. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
14. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
15. Kamvysselis,K., Patterson,N., Birren,B., Berger,B. and Lander,E. (2003) Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. RECOMB, 2003, 157-166.
16. 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.
17. Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
18. McGuire,A.M., Hughes,J.D. and Church,G.M. (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res., 10, 744-757.
19. Pevzner,P.A. and Sze,S.H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 269-278.
20. Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
21. Robison,K., McGuire,A.M. and Church,G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol., 284, 241-254.
22. Shabalina,S.A., Ogurtsov,A.Y., Kondrashov,V.A. and Kondrashov,A.S. (2001) Selective constraint in intergenic regions of human and mouse genomes. Trends Genet., 17, 373-376.
23. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
24. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
25. Stormo,G.D. and Fields,D.S. (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci., 23, 109-113.
26. Stormo,G.D. and Hartzell,G.W., 3rd (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
27. Sze,S.H., Gelfand,M.S. and Pevzner,P.A. (2002) Finding weak motifs in DNA sequences. Pac. Symp. Biocomput., 235-246.
28. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
29. Wasserman,W.W., Palumbo,M., Thompson,W., Fickett,J.W. and Lawrence,C.E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat. Genet., 26, 225-228.
30. Workman,C.T. and Stormo,G.D. (2000) ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput., 467-478.