TY - JOUR
T1 - The YEASTRACT database
T2 - An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
AU - Teixeira, Miguel Cacho
AU - Monteiro, Pedro Tiago
AU - Guerreiro, Joana Fernandes
AU - Goncalves, Joana Pinho
AU - Mira, Nuno Pereira
AU - dos Santos, Sandra Costa
AU - Cabrito, Tania Rodrigues
AU - Palma, Margarida
AU - Costa, Catarina
AU - Francisco, Alexandre Paulo
AU - Madeira, Sara Cordeiro
AU - Oliveira, Arlindo Limede
AU - Freitas, Ana Teresa
AU - Sa-Correia, Isabel
PY - 2014/1
Y1 - 2014/1
N2 - 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.
AB - 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.
U2 - 10.1093/nar/gkt1015
DO - 10.1093/nar/gkt1015
M3 - Article
SN - 0305-1048
VL - 42
SP - D161-D166
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -