9th Annual Workshop, October 28-31, 1999
Co-sponsored by the U.S. Department of Energy
TRANSFAC: an integrated system for gene expression regulation
E. Wingender, X. Chen, H. Karas, A. Kel, I. Liebich, V. Matys, T. Meinhardt, M. Pruess, I. Reuter, and F. Schacherer
GBF, Molecular Bioinformatics of Gene Regulation, Braunschweig, Germany
The "post-genomic" era of research will focus largely on so-called "functional genomics", assigning functional properties to all genes of an organism. Part of these efforts is the mass generation of gene expression data due to new experimental technologies such as the application of DNA microarrays. Standardized storage of these data is required to avoid unnecessary duplication of cost-intensive work and to draw an integrated view of the overall gene expression profile of, e. g., the human organism. We therefore started to develop an integrated system for a unifying view on "expression states", defined by organ / cell types, their developmental stages, and conditions (e. g. hormonal induction). The system integrates five databases which we have developed: On the first level, the database TRANSFAC which provides data on transcriptional control, is integrated with a newly developed database on pathological mutations in transcription control components (PathoDB) and with a database on scaffold / matrix attachment regions (S/MARt DB). At a second level, the systems incorporates a data resource on signal transduction components and reactions (TRANSPATH) and another one on (human) organs, cell types, physiological systems and their developmental stages (CYTOMER). As an example, we started to apply our ideas on "mapping" the expression patterns of transcription factors as they are represented in the TRANSFAC database.