YEASTRACT (Yeast Search for Transcriptional Regulators
And Consensus Tracking) is a curated repository of more than
206000 regulatory associations between transcription factors (TF) and target genes
in Saccharomyces cerevisiae, based on more than 1300 bibliographic references.
It also includes the description of 326 specific DNA binding sites shared among 113
characterized TFs. Further information about each Yeast gene has been
extracted from the Saccharomyces Genome Database (SGD) as per the latest release,
revision 7785, from Apr 27, 2013. For each gene the associated Gene Ontology (GO)
terms and their hierarchy in GO was obtained from the GO consortium as per the
OBO flat file from May 04, 2013. Currently, YEASTRACT maintains a total of
7130 terms from GO. The nucleotide sequences of the promoter and coding regions
for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT).
All the information in YEASTRACT is updated regularly to match the latest
data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory
YEASTRACT includes DISCOVERER, a set of tools
that can be used to identify complex motifs found to be over-represented in
the promoter regions of co-regulated genes. DISCOVERER is based on the
These algorithms take as input a list of genes and identify over-represented
motifs, which can then be compared with transcription factor binding sites
described in the YEASTRACT database.
Facilities are also provided to enable the exploitation of the gathered data
when solving a number of biological questions, as exemplified in the Tutorial.
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 and the transcription factor binding sites described in the literature.
The system also provides a 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
YEASTRACT provides a set of queries to search and retrieve important biological
information from the gathered data and to predict transcription regulation networks
in yeast from data emerging from gene-by-gene analysis or global approaches.
The Yeastract database has been updated recently with:
- Updated Gene Ontology terms;
- Updated Gene information from Saccharomyces Genome Database;
- New PBM/MITOMI consensus sequences;
- New gene ranking algorithm;
- New curated regulatory information!
(environmental condition, association type and evidence code)