YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.
The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) information system (http://www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2010, this database contains over 48,200 regulatory associations between transcription factors (TFs) and target genes, including 298 specific DNA-binding sites for 110 characterized TFs. All regulatory associations stored in the database were revisited and detailed information on the experimental evidences that sustain those associations was added and classified as direct or indirect evidences. The inclusion of this new data, gathered in response to the requests of YEASTRACT users, allows the user to restrict its queries to subsets of the data based on the existence or not of experimental evidences for the direct action of the TFs in the promoter region of their target genes. Another new feature of this release is the availability of all data through a machine readable web-service interface. Users are no longer restricted to the set of available queries made available through the existing web interface, and can use the web service interface to query, retrieve and exploit the YEASTRACT data using their own implementation of additional functionalities. The YEASTRACT information system is further complemented with several computational tools that facilitate the use of the curated data when answering a number of important biological questions. Since its first release in 2006, YEASTRACT has been extensively used by hundreds of researchers from all over the world. We expect that by making the new data and services available, the system will continue to be instrumental for yeast biologists and systems biology researchers.
Abdulrehman
Dário
D
INESC-ID, Knowledge Discovery and Bioinformatics Group, R Alves Redol 9, 1000-029 Lisbon, Portugal.
Monteiro
Pedro Tiago
PT
Teixeira
Miguel Cacho
MC
Mira
Nuno Pereira
NP
Lourenço
Artur Bastos
AB
dos Santos
Sandra Costa
SC
Cabrito
Tânia Rodrigues
TR
Francisco
Alexandre Paulo
AP
Madeira
Sara Cordeiro
SC
Aires
Ricardo Santos
RS
Oliveira
Arlindo Limede
AL
Sá-Correia
Isabel
I
Freitas
Ana Teresa
AT
D001665:Binding Sites; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D020407:Internet; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors