Summary
Bioinformatic and experimental analyses of promoter regions are available for a long time. Finding of the transcription factor binding sites (TFBSs), however, by either method still faces a number of problems. For example, because of the ambiguity of binding of transcription factors, the number of false-positives and -negatives can be unexpectedly high in these sequence analyses. We can assume that evolutionary conserved motifs or regions in the promoters of the homologous genes function as TFBSs. Thus, a comparative genomic approach can provide a partial resolution for the problem previously outlined.
This chapter describes application of the DoOP database and the DoOPSearch web tools for such a comparative genomic analysis. Orthologous promoter sequences and conserved motifs can be extracted from the DoOP database for further analysis. The web-based tools of the DoOPSearch webpage can be used for searching and comparing conserved motifs. Using these tools, it is possible to compare short sequences with conserved motifs, to map conserved motifs into a longer promoter region, or find sequence patterns in different sets of promoter sequences.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Schmid, C. D., Perier, R., Praz, V., and Bucher, P. (2006) EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res. 34, D82–D85.
Papatsenko, D. and Levine, M. (2005) Computational identification of regulatory DNAs underlying animal development. Nat. Methods 2, 529–534.
Prakash, A. and Tompa, M. (2005) Discovery of regulatory elements in vertebrates through comparative genomics. Nat. Biotechnol. 23, 1249–1256.
Barta, E., Sebestyón, E., Pálfy, T. B., Téth, G., Ortutay, C. P., and Patthy, L. (2005) DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. Nucleic Acids Res. 33, D86–D90.
Birney, E., Andrews, D., Caccamo, M., et al. (2006) Ensembl 2006. Nucleic Acids Res. 34, D556–D561.
Matys, V., Kel-Margoulis, O. V., Fricke, E., et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108–D110.
Vlieghe, D., Sandelin, A., De Bleser, P. J., et al. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34, D95–D97.
Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3’ UTRs by comparison of several mammals. Nature 434, 338–345.
Robertson, G., Bilenky, M., Lin, K., et al. (2006) cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res. 34, D68–73.
Dieterich, C., Grossmann, S., Tanzer, A., et al. (2005) Comparative promoter region analysis powered by CORG. BMC Genomics 6, 24.
Zhao, F., Xuan, Z., Liu, L., and Zhang, M. Q. (2005) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res. 33, D103–D107.
Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277.
Acknowledgments
I am grateful to Dr. Ferenc Marincs for critical reading of the manuscript and for his helpful suggestions.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Barta, E. (2007). Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_20
Download citation
DOI: https://doi.org/10.1007/978-1-59745-514-5_20
Publisher Name: Humana Press
Print ISBN: 978-1-58829-693-1
Online ISBN: 978-1-59745-514-5
eBook Packages: Springer Protocols