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

Abstract

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.

Figure 1

Main entities in the database model and their relationships.

Figure 2

(a) Graphic display of the transcription factor-binding sites found to occur in the promoter regions of FLR1 and TPO1 genes. (b) The table below contains the list of all transcription factors identified as potential regulators of FLR1 or TPO1. By selecting a subset of transcription factors known to be involved in multidrug resistance, it is possible to generate a simplified graphic display.

Figure 3

Output of a search for DNA motifs query. A set of DNA motifs, corresponding to the Yap1p-binding sites documented in the literature, was searched for in the promoter region of a Yap1p-documented target gene, FLR1 [(9) and other references displayed in the database]. The figure shows the occurrences of the given DNA motifs in the promoter region of this gene. Information on the gene function (‘Description’) and a link to the SGD page dedicated to FLR1 are also available.