Computational identification of regulatory DNAs underlying animal development

Nature Methods

Volumn 2, Issue 7, 2005, Pages 529-534

  Papatsenko, Dmitri ^a   Levine, Michael ^a  

^a University of California Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GENOMIC DNA; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; LABORATORY DIAGNOSIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REGULATORY DNA SEQUENCE; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA; GENES, REGULATOR; GROWTH AND DEVELOPMENT;

ANIMALIA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; MUS MUSCULUS;

EID: 23644436149     PISSN: 15487091     EISSN: None     Source Type: Journal    
DOI: 10.1038/nmeth0705-529     Document Type: Article

References (15)

1. Ohler, U. & Niemann, H. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 17, 56-60 (2001).
2. Bejerano, G., Siepel, A.C., Kent, W.J. & Haussler, D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat. Methods 2, 535-545 (2005).
3. Wasserman, W.W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5, 276-287 (2004).
4. Markstein, M., Markstein, P., Markstein, V. & Levine, M.S. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 99, 763-768 (2002).
5. Lifanov, A.P., Makeev, V.J., Nazina, A.G. & Papatsenko, D.A. Homotypic regulatory clusters in Drosophila. Genome Res. 13, 579-588 (2003).
6. Schroeder, M.D. et al. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2, E271 (2004).
7. Berman, B.P. et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 5, R61 (2004).
8. Kondrakhin, Y.V., Kel, A.E., Kolchanov, N.A., Romashchenko, A.G. & Milanesi, L. Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11, 477-488 (1995).
9. Crowley, E.M., Roeder, K. & Bina, M. A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol. 268, 8-14 (1997).
10. Wagner, A. A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 25, 3594-3604 (1997).
11. Pickert, L., Reuter, I., Klawonn, F. & Wingender, E. Transcription regulatory region analysis using signal detection and fuzzy clustering. Bioinformatics 14, 244-251 (1998).
12. Ovcharenko, I. et al. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15, 137-145 (2005).
13. Nelson, C.E., Hersh, B.M. & Carroll, S.B. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol. 5, R25 (2004).
14. Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, & Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 15, 737-41 (2005).
15. Stathopoulos, A. & Levine, M. Whole-genome analysis of Drosophila gastrulation. Curr. Opin. Genet. Dev. 14, 477-84 (2004).