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The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
- Source :
- Nucleic Acids Research
- Publication Year :
- 2013
- Publisher :
- Oxford University Press, 2013.
-
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.
- Subjects :
- I. Nucleic acid sequence, structure and regulation
Saccharomyces cerevisiae Proteins
Systems biology
Gene regulatory network
Saccharomyces cerevisiae
Biology
computer.software_genre
Genome
03 medical and health sciences
Gene Expression Regulation, Fungal
Databases, Genetic
Genetics
Gene Regulatory Networks
Regulatory Elements, Transcriptional
DNA, Fungal
Transcription factor
Gene
030304 developmental biology
Regulation of gene expression
0303 health sciences
Internet
Binding Sites
Database
030302 biochemistry & molecular biology
DNA binding site
Regulon
Genome, Fungal
computer
Software
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 13624962 and 03051048
- Volume :
- 42
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....2f04053e8acf5eb46df229204c84b1db