Using hexamers to predict cis-regulatory motifs in Drosophila

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Chan, Bob Y ^a   Kibler, Dennis ^a  

^a Ringgold Standard Institution Informatics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS-REGULATORY MODULES; COMPUTATIONAL TECHNIQUE; DATA SET; MEGABASE; PREDICTION ALGORITHMS; REGULATORY ELEMENTS; REGULATORY SYSTEMS; TARGET GENES;

ALGORITHMS;

GENE EXPRESSION;

DNA;

ALGORITHM; ANIMAL TISSUE; ARTICLE; BINDING SITE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DNA SEQUENCE; DROSOPHILA; EMBRYO; ENHANCER REGION; GENE CONTROL; GENE TARGETING; NONHUMAN; PREDICTION; PROMOTER REGION; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; PROCEDURES; PROTEIN MOTIF;

ANIMALIA; EUKARYOTA;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; DROSOPHILA; GENE EXPRESSION REGULATION; SEQUENCE ANALYSIS, DNA;

EID: 27744473016     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-262     Document Type: Article

References (35)

1. Davidson EH, McClay DR, Hood L: Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A 2003, 100(4):1475-1480.
2. Qiu P: Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun 2003, 309(3):495-501.
3. Laimins LA, Gruss P, Pozzatti R, Khoury G: Characterization of enhancer elements in the long terminal repeat of Moloney murine sarcoma virus. J Virol 1984, 49(1):183-189.
4. Qin Y, Kong LK, Poirier C, Truong C, Overbeek PA, Bishop CE: Long-range activation of Sox9 in Odd Sex (Ods) mice. Hum Mol Genet 2004, 13(12):1213-1218.
5. Wasserman WW, Fickett JW: Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278(1):167-181.
6. Krivan W, Wasserman WW: A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11(9):1559-1566.
7. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002, 99(2):757-762.
8. Bailey TL, Noble WS: Searching for statistically significant regulatory modules. Bioinformatics 2003, 19 Suppl 2:II16-II25.
9. Rajewsky N, Vergassola M, Gaul U, Siggia ED: Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 2002, 3(1):30.
10. Sinha S, van Nimwegen E, Siggia ED: A probabilistic method to detect regulatory modules. Bioinformatics 2003, 19 Suppl 1:i292-301.
11. Frith MC, Li MC, Weng Z: Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res 2003, 31(13):3666-3668.
12. Johansson O, Alkema W, Wasserman WW, Lagergren J: Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Bioinformatics 2003, 19 Suppl 1:i169-176.
13. Gupta M, Liu JS: De novo cis-regulatory module elicitation for eukaryotic genomes. Proc Natl Acad Sci U S A 2005, 102(20):7079-7084.
14. Rebeiz M, Reeves NL, Posakony JW: SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. Proc Natl Acad Sci U S A 2002, 99(15):9888-9893.
15. Markstein M, Markstein P, Markstein V, Levine MS: Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A 2002, 99(2):763-768.
16. Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA: Homotypic regulatory clusters in Drosophila. Genome Res 2003, 13(4):579-588.
17. Tagle DA, Koop BF, Goodman M, Slightom JL, Hess DL, Jones RT: Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol 1988, 203(2):439-455.
18. Blanchette M, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 2002, 12(5):739-748.
19. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM: Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003, 299(5611):1391-1394.
20. Sumiyama K, Kim CB, Ruddle FH: An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 2001, 71(2):260-262.
21. Grad YH, Roth FP, Halfon MS, Church GM: Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics 2004, 20(16):2738-2750.
22. Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW: Identification of conserved regulatory elements by comparative genome analysis. J Biol 2003, 2(2):13.
23. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002, 12(5):832-839.
24. Yuh CH, Brown CT, Livi CB, Rowen L, Clarke PJ, Davidson EH: Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol 2002, 246(1):148-161.
25. Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15(7-8):563-577.
26. Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296(5):1205-1214.
27. van Helden J, Andre B, Collado-Vides J: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 1998, 281(5):827-842.
28. Abnizova I, te Boekhorst R, Walter K, Gilks WR: Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test. BMC Bioinformatics 2005, 6(1):109.
29. Hutchinson GB: The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput Appl Biosci 1996, 12(5):391-398.
30. Nazina AG, Papatsenko DA: Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. BMC Bioinformatics 2003, 4(1):65.
31. Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U: Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol 2004, 2(9):E271.
32. [http://webdisk.berkeley.edu/~dap5/]
33. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R et al: The TRANSFAC system on gene expression regulation. Nucleic Acids Res 2001, 29(1):281-283.
34. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16(5):412-424.
35. Mitchell TM: Machine Learning. New York: McGraw-Hill; 1997.