Abstract
A major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. Even though a variety of sequences have been shown to interact with the transcription factors that bind DNA, extensive work is needed to discover and classify regulatory “codes” and to elucidate the role played by the sequence context of genomic DNA in the regulation of genes. Databases of sequence elements extracted from regulatory regions may facilitate this process. This report provides a Toolkit and instructions for creating a database for collecting and analyzing 9-base elements (9-mers) from a large collection of DNA sequences. A reference set consisting of all possible 9-mers is included for extracting potential control elements, irrespective of their orientation and order in DNA.
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References
International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
Venter, J. C., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Collins, F. S., Green, E. D., Guttmacher, A. E.,and Guyer, M. S. (2003) A vision for the future of genomics research. Nature 422, 835–847.
Bina, M., Wyss, P., Ren, W., et al. (2004) Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics 84, 929–940.
Hutchinson, G. B. (1996) The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Appl. Biosci. 12, 391–398.
Marino-Ramirez, L., Spouge, J. L., Kanga, G. C., and Landsman, D. (2004) Statis-tical analysis of over-represented words in human promoter sequences. Nucleic Acids Res. 32, 949–958.
FitzGerald, P. C., Shlyakhtenko, A., Mir, A. A., and Vinson, C. (2004) Clustering of DNA sequences in human promoters. Genome Res. 8, 1562–1574.
Trinklein, N. D., Aldred, S. J, Saldanha, A. J., and Myers, R. M. (2003) Identifi-cation and functional analysis of human transcriptional promoters. Genome Res. 13, 308–312.
Kent, W. J., Sugnet, C. W., Furey, T. S., et al. (2002) The human genome browser at UCSC. Genome Res. 12, 996–1006.
Karolchik, D., Baertsch, R., Diekhans, M., et al. (2003) University of California Santa Cruz. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51–54.
Karolchik, D., Hinrichs, A. S., Furey, T. S., et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32 (Database issue), D493–496.
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Wyss, P., Lazarus, S.A., Bina, M. (2006). A Program Toolkit for the Analysis of Regulatory Regions of Genes. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:135
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DOI: https://doi.org/10.1385/1-59745-097-9:135
Publisher Name: Humana Press
Print ISBN: 978-1-58829-575-0
Online ISBN: 978-1-59745-097-3
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