title: The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.
abstract: The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2013, this database contains over 200,000 regulatory associations between transcription factors (TFs) and target genes, including 326 DNA binding sites for 113 TFs. All regulatory associations stored in YEASTRACT were revisited and new information was added on the experimental conditions in which those associations take place and on whether the TF is acting on its target genes as activator or repressor. Based on this information, new queries were developed allowing the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. This release further offers tools to rank the TFs controlling a gene or genome-wide response by their relative importance, based on (i) the percentage of target genes in the data set; (ii) the enrichment of the TF regulon in the data set when compared with the genome; or (iii) the score computed using the TFRank system, which selects and prioritizes the relevant TFs by walking through the yeast regulatory network. We expect that with the new data and services made available, the system will continue to be instrumental for yeast biologists and systems biology researchers.
authors.affiliation: Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; IBB-Institute for Biotechnology and BioEngineering, Centre for Biological and Chemical Engineering, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal and INESC-ID, Knowledge Discovery and Bioinformatics Group, R. Alves Redol, 9, 1000-029 Lisbon, Portugal.
authors.forename: Miguel Cacho
authors.initials: MC
authors.lastname: Teixeira
authors.forename: Pedro Tiago
authors.initials: PT
authors.lastname: Monteiro
authors.forename: Joana Fernandes
authors.initials: JF
authors.lastname: Guerreiro
authors.forename: Joana Pinho
authors.initials: JP
authors.lastname: Gonçalves
authors.forename: Nuno Pereira
authors.initials: NP
authors.lastname: Mira
authors.forename: Sandra Costa
authors.initials: SC
authors.lastname: dos Santos
authors.forename: Tânia Rodrigues
authors.initials: TR
authors.lastname: Cabrito
authors.forename: Margarida
authors.initials: M
authors.lastname: Palma
authors.forename: Catarina
authors.initials: C
authors.lastname: Costa
authors.forename: Alexandre Paulo
authors.initials: AP
authors.lastname: Francisco
authors.forename: Sara Cordeiro
authors.initials: SC
authors.lastname: Madeira
authors.forename: Arlindo Limede
authors.initials: AL
authors.lastname: Oliveira
authors.forename: Ana Teresa
authors.initials: AT
authors.lastname: Freitas
authors.forename: Isabel
authors.initials: I
authors.lastname: Sá-Correia
mesh_terms: D001665:Binding Sites; D004271:DNA, Fungal / Q000378:metabolism*; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors