Abstract
The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2013, this database contains over 200 000 regulatory associations between transcription factors (TFs) and target genes, including 326 DNA binding sites for 113 TFs. All regulatory associations stored in YEASTRACT were revisited and new information was added on the experimental conditions in which those associations take place and on whether the TF is acting on its target genes as activator or repressor. Based on this information, new queries were developed allowing the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. This release further offers tools to rank the TFs controlling a gene or genome-wide response by their relative importance, based on (i) the percentage of target genes in the data set; (ii) the enrichment of the TF regulon in the data set when compared with the genome; or (iii) the score computed using the TFRank system, which selects and prioritizes the relevant TFs by walking through the yeast regulatory network. We expect that with the new data and services made available, the system will continue to be instrumental for yeast biologists and systems biology researchers.
Highlights
Since its release in 2006, the YEASTRACT (YEAst Search for Transcriptional Regulators And Consensus Tracking; http://www.yeastract.com) database [1] provides to the public up-to-date information on documented regulatory associations between transcription factors (TFs) and target genes, as well as between TFs and DNA binding sites, in Saccharomyces cerevisiae
Besides providing tools for promoter analysis in yeast, YEASTRACT is, to our knowledge, the single information system that offers a complete integration of all the experimentally validated transcriptional regulatory data ever published for S. cerevisiae
Evidence’ classification was attributed to experiments such as the comparative analysis of gene expression changes occurring in response to the deletion, mutation or overexpression of a given TF, based on experimental techniques that include northern blotting, quantitative
Summary
Since its release in 2006, the YEASTRACT (YEAst Search for Transcriptional Regulators And Consensus Tracking; http://www.yeastract.com) database [1] provides to the public up-to-date information on documented regulatory associations between transcription factors (TFs) and target genes, as well as between TFs and DNA binding sites, in Saccharomyces cerevisiae. Besides providing tools for promoter analysis in yeast, YEASTRACT is, to our knowledge, the single information system that offers a complete integration of all the experimentally validated transcriptional regulatory data ever published for S. cerevisiae.
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