This work was partially supported by the Portuguese Fundação para a Ciência e Tecnologia through POSC and PDTC, namelly via the following project grants:
POSC/EIA/57398/2004: DBYeast: Infrastructures and algorithms for analysis and identification of gene regulatory networks PDTC/BIO/56838/2004: Insights into the complex regulatory networks acting in Yeast cells challenged with drugs/chemical stresses: genome-wide expression approaches supported by bioinformatics

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The information about Yeast genes other than documented regulations, potential regulations and the TF binding sites contained in YEASTRACT are gathered from; Saccharomyces Genome Database (SGD), Gene Ontology (GO) Consortium and Regulatory Sequence Analysis (RSA) Tools.

We acknowledge SGD for making those file available to the public:

• The gene association file available to download from the Gene Name List Web page at SGD was parsed to get the systematic, standard and alias names for Yeast genes and GO terms associated to them [1].
  ftp://ftp.yeastgenome.org/yeast/data_download/literature_curation/gene_association.sgd.gz
• The file from ftp download areas at SGD, that contains the translations of all systematically named ORFs, including Verified, Uncharacterized, and Dubious ORFs and pseudogenes was parsed to get amino acid sequence for gene products [2].
  ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/orf_protein/orf_trans.fasta.gz

We acknowledge GO Consortium for making GO database and vocabularies freely available to the public:

• The single OBO format flat file by GO consortium providing ontologies and terms definitions was parsed to identify level and logical relationships between the GO terms associated to each gene in the GO hierarchy [3].
  http://www.geneontology.org/ontology/gene_ontology.obo

We acknowledge the RSAT team for providing free access to the different functionalities of the RSA Tools to academic users:

• The Sequence Retrieval functionality provided by RSA Tools was used to retrieve nucleotide sequences for the genes and promoter sequences for the Yeast genes [4].

We are grateful to colleagues and friends from the yeast community for their encouragement and suggestions. A very special thanks is due to André Goffeau.

References:
1. Hong EL, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Livstone MS, Nash R, Oughtred R, Park J, Skrzypek M, Starr B, Andrada R, Binkley G, Dong Q, Hitz BC, Miyasato S, Schroeder M, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, and Cherry JM.
"Saccharomyces Genome Database"
ftp://ftp.yeastgenome.org/yeast/data_download/literature_curation/gene_association.sgd.gz
(16 June, 2007).

2. Hong EL, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Livstone MS, Nash R, Oughtred R, Park J, Skrzypek M, Starr B, Andrada R, Binkley G, Dong Q, Hitz BC, Miyasato S, Schroeder M, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, and Cherry JM.
"Saccharomyces Genome Database"
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/orf_protein/orf_trans.fasta.gz
(21 June 2007).
 
3. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29.

4. Van Helden, J., André B. & Collado-Vides, J. (2000). A web site for the computational analysis of yeast regulatory sequences. Yeast 16(2), 177-187.