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Nucleic Acids Research Advance Access published online on November 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm976
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© 2007
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

Pedro T. Monteiro1,3, Nuno D. Mendes1,3, Miguel C. Teixeira2,3, Sofia d’Orey1, Sandra Tenreiro2,3, Nuno P. Mira2,3, Hélio Pais1, Alexandre P. Francisco1,3, Alexandra M. Carvalho1,3, Artur B. Lourenço2,3, Isabel Sá-Correia2,3, Arlindo L. Oliveira1,3 and Ana T. Freitas1,3,*

1INESC-ID, Knowledge Discovery and Bioinformatics Group, R. Alves Redol, 9, 1000-029 Lisbon, 2IBB-Institute for Biotechnology and BioEngineering, Centre for Biological and Chemical Engineering, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon and 3Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal

*To whom correspondence should be addressed. Tel: +351 213100384; Fax: +351 213145843; Email: atf{at}inesc-id.pt

Received September 14, 2007. Revised October 17, 2007. Accepted October 18, 2007.

The Yeast search for transcriptional regulators and consensus tracking (YEASTRACT) information system (www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in September 2007, this database contains over 30 990 regulatory associations between Transcription Factors (TFs) and target genes and includes 284 specific DNA binding sites for 108 characterized TFs. Computational tools are also provided to facilitate the exploitation of the gathered data when solving a number of biological questions, in particular the ones that involve the analysis of global gene expression results. In this new release, YEASTRACT includes DISCOVERER, a set of computational tools that can be used to identify complex motifs over-represented in the promoter regions of co-regulated genes. The motifs identified are then clustered in families, represented by a position weight matrix and are automatically compared with the known transcription factor binding sites described in YEASTRACT. Additionally, in this new release, it is possible to generate graphic depictions of transcriptional regulatory networks for documented or potential regulatory associations between TFs and target genes. The visual display of these networks of interactions is instrumental in functional studies. Tutorials are available on the system to exemplify the use of all the available tools.


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