Michael, Holger;Christensen, Maik;Goessling, Ellen;Wingender, Edgar

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Title: TSM, the TRANSFAC Saccharomyces Module	P106
Michael, Holger; Christensen, Maik; Goessling, Ellen; Wingender, Edgar hom@gbf.de GBF - Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany; Biobase Biological Databases GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany

The early completion of the whole genome sequence has firmly established yeast as the best investigated eukaryotic organism. Subsequent large-scale experiments are aiming at the genome-wide elucidation of gene functions (see e.g. Gavin et al., 2002, or Simon et al., 2002). In order to make sense of the vast amount of data and extracting conclusions and hypotheses that are biologically meaningful, sophisticated systems of knowledge representation are needed. The TRANSFAC database, part of the TRANSFAC system, is a relational database that comprises data on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles (Wingender et al., 2001). Many transcription factors bind to sites with related properties. From these binding sites, nucleotide distribution matrices can be constructed. This kind of information is stored in the MATRIX table, which comprises DNA-binding profiles for individual or groups of transcription factors. These data are a valuable information resource in itself and also serve as a basis for dedicated bioinformatics software searching for putative transcription factor binding sites in the genome. We have collected data on all known yeast transcription factors, their binding sites and the regulated genes in TRANSFAC. These yeast data form a separate subset, the TRANSFAC Saccharomyces Module (TSM). TSM is available to the public as a runtime information resource at [http:/transfac.gbf.de]. Furthermore, it is being integrated into the Comprehensive Yeast Genome Database (CYGD), a joint European effort combining several yeast laboratories and including specialized databases. CYGD is maintained at the Munich Information Center for Protein Sequences, MIPS [http://mips.gsf.de/proj/yeast/CYGD/db/index.html].

[1] Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, G.: Functional organization of the yeast proteome by systematic analysis of protein complexes.
Nature 415,141-147 (2002).
[2] Simon, I., Barnett, J., Hannett, N., Harbison, C. T., Rinaldi, N. J., Volkert, T. L., Wyrick, J. J., Zeitlinger, J., Gifford, D. K., Jaakkola, T. S., Young, R. A.: Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106,697-708 (2002).
[3] Wingender E., Chen X., Fricke E., Geffers R., Hehl R., Liebich I., Krull M., Matys V., Michael H., Ohnhäuser R., Prüß M., Schacherer F., Thiele S., Urbach S.: The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29: 281-283 (2001).