@article{teixeira_et_al_nar_13,
    author = {M.C. Teixeira, P.T. Monteiro, J. Guerreiro, J.P. Gon\c{c}alves, N.P. Mira, S.C. dos Santos, T.R. Cabrito, M. Palma, C. Costa, A.P. Francisco, S.C. Madeira, A.L. Oliveira, A.T. Freitas, I. S\'a-Correia},
    title = {The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in \textit{Saccharomyces cerevisiae}},
    journal = {Nucleic Acids Research},
    volume = {42},
    number = {D1},
    pages = {D161-D166},
    year = {2014},
	doi = {10.1093/nar/gkt1015},
    abstract = {The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT -
www.yeastract.com) information system is a tool for the analysis and prediction of transcription
regulatory associations at the gene and genomic levels in Saccharomyces cerevisiae. Last updated in
June 2013, this database contains nearly 206.000 regulatory associations between Transcription Factors
(TFs) and target genes, including 326 specific DNA binding sites for 113 characterized TFs. All
regulatory associations stored in the database were revisited and new information was added on the
experimental conditions in which those associations take place and on whether the transcription factor
is acting upon its target genes as an activator or repressor. This new information, long requested by
YEASTRACT users, enabled the development of new queries in which searches can be filtered based
on the selection of specific environmental conditions, experimental evidence or positive/negative
regulatory effect. Another new feature of this release is the offer of a set of tools to enable the
prediction of the TFs involved in the regulation of a gene or genome-wide transcriptional response,
while ranking those TFs in order of their relative importance. Three ranking options are now offered
including ranking by: 1) the percentage of target genes in the dataset; 2) the enrichment of the TF
regulon in the dataset when compared to the genome; and 3) the score computed using the TFRank
system, which selects and prioritizes the relevant TFs by walking through the yeast regulatory network.
Finally, this new release provides more intuitive and interactive visualization tools for the
representation of TF regulatory networks built by its users. Since its first release in 2006,
YEASTRACT has been extensively used by hundreds of researchers from all over the world and
receives around 2.000 monthly visits. 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.}
}