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Nucleic Acids Research 2006 34(Database Issue):D446-D451; doi:10.1093/nar/gkj013
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Nucleic Acids Research, 2006, Vol. 34, Database issue D446-D451
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae

Miguel C. Teixeira1, Pedro Monteiro2, Pooja Jain2, Sandra Tenreiro1, Alexandra R. Fernandes1, Nuno P. Mira1, Marta Alenquer1, Ana T. Freitas2,3, Arlindo L. Oliveira2,3 and Isabel Sá-Correia1,3,*

1Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico Avenida Rovisco Pais, 1049-001 Lisbon, Portugal 2INESC-ID R. Alves Redol, 9, 1000 Lisbon, Portugal 3Instituto Superior Técnico Avenida Rovisco Pais, 1049-001, Lisbon, Portugal

*To whom correspondence should be addressed. Tel: +351 218417682; Fax: +351 218489199; Email: isacorreia{at}ist.utl.pt

Received July 27, 2005. Revised September 14, 2005. Accepted September 14, 2005.

We present the YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT; www.yeastract.com) database, a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. This database is a repository of 12 346 regulatory associations between transcription factors and target genes, based on experimental evidence which was spread throughout 861 bibliographic references. It also includes 257 specific DNA-binding sites for more than a hundred characterized transcription factors. Further information about each yeast gene included in the database was obtained from Saccharomyces Genome Database (SGD), Regulatory Sequences Analysis Tools and Gene Ontology (GO) Consortium. Computational tools are also provided to facilitate the exploitation of the gathered data when solving a number of biological questions as exemplified in the Tutorial also available on the system. YEASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs, such as those found to be over-represented in the promoter regions of co-regulated genes, and the transcription factor-binding sites described in the literature. The system also provides an useful mechanism for grouping a list of genes (for instance a set of genes with similar expression profiles as revealed by microarray analysis) based on their regulatory associations with known transcription factors.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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