YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

TLDR

YEASTRACT is a curated database of over 30,000 transcription factor–gene regulatory associations and 284 DNA binding sites in Saccharomyces cerevisiae, supplemented with computational tools for analyzing global gene expression data. The new release introduces DISCOVERER, a set of tools that identify over‑represented promoter motifs in co‑regulated genes and generate graphical depictions of transcriptional regulatory networks. DISCOVERER clusters identified motifs into families represented by position‑weight matrices, automatically compares them to known TF binding sites in YEASTRACT, and visualizes the resulting regulatory networks to aid functional studies.

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.