The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.
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.
Teixeira
Miguel C
MC
Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal.
Monteiro
Pedro
P
Jain
Pooja
P
Tenreiro
Sandra
S
Fernandes
Alexandra R
AR
Mira
Nuno P
NP
Alenquer
Marta
M
Freitas
Ana T
AT
Oliveira
Arlindo L
AL
Sá-Correia
Isabel
I
D001665:Binding Sites; D019295:Computational Biology; D004271:DNA, Fungal / Q000737:chemistry / Q000378:metabolism; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D020407:Internet; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors