title: YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.
abstract: 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.
authors.affiliation: INESC-ID, Knowledge Discovery and Bioinformatics Group, R. Alves Redol, 9, 1000-029 Lisbon, Portugal.
authors.forename: Pedro T
authors.initials: PT
authors.lastname: Monteiro
authors.forename: Nuno D
authors.initials: ND
authors.lastname: Mendes
authors.forename: Miguel C
authors.initials: MC
authors.lastname: Teixeira
authors.forename: Sofia
authors.initials: S
authors.lastname: d'Orey
authors.forename: Sandra
authors.initials: S
authors.lastname: Tenreiro
authors.forename: Nuno P
authors.initials: NP
authors.lastname: Mira
authors.forename: Hélio
authors.initials: H
authors.lastname: Pais
authors.forename: Alexandre P
authors.initials: AP
authors.lastname: Francisco
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Carvalho
authors.forename: Artur B
authors.initials: AB
authors.lastname: Lourenço
authors.forename: Isabel
authors.initials: I
authors.lastname: Sá-Correia
authors.forename: Arlindo L
authors.initials: AL
authors.lastname: Oliveira
authors.forename: Ana T
authors.initials: AT
authors.lastname: Freitas
mesh_terms: D001665:Binding Sites; D030561:Databases, Nucleic Acid; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D020407:Internet; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors