The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.
We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata Upon data retrieval from hundreds of publications, followed by curation, the database currently includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species. Following the structure used for the YEASTRACT database, PathoYeastract makes available bioinformatics tools that enable the user to exploit the existing information to predict the TFs involved in the regulation of a gene or genome-wide transcriptional response, while ranking those TFs in order of their relative importance. Each search can be filtered based on the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. Promoter analysis tools and interactive visualization tools for the representation of TF regulatory networks are also provided. The PathoYeastract database further provides simple tools for the prediction of gene and genomic regulation based on orthologous regulatory associations described for other yeast species, a comparative genomics setup for the study of cross-species evolution of regulatory networks.
Department of Computer Science and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal Pedro.Tiago.Monteiro@tecnico.pt.|INESC-ID, R. Alves Redol, 9, 1000-029 Lisbon, Portugal.
Pedro Tiago
PT
Monteiro
Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.|iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
Pedro
P
Pais
Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.|iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
Catarina
C
Costa
INESC-ID, R. Alves Redol, 9, 1000-029 Lisbon, Portugal.|Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.|iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
Sauvagya
S
Manna
Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.|iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
Isabel
I
Sá-Correia
Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal mnpct@tecnico.ulisboa.pt.|iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
Miguel Cacho
MC
Teixeira
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D064878:Web Browser; D015003:Yeasts / Q000235:genetics*
D014157:Transcription Factors