TRANSFAC®
The TRANSFAC® database has been constructed to model the interaction of eukaryotic transcription factors with their DNA-binding sites and how this affects gene expression. At its core are the three tables FACTOR, SITE, and GENE. A link between FACTOR and SITE indicates the interaction (binding) between them. Experimental evidence for this interaction is given in the SITE entry in form of the method (gel shift, footprinting analysis, ...) which was used to show the binding and the cell from which the factor was derived (factor source). On the basis of those, method and cell, a quality value is given to describe the "confidence" with which a binding activity could be assigned to a specific factor. When a number of binding sites have been collected for a factor, the site sequences are aligned and nucleotide distribution matrices are derived (MATRIX). These matrices are used by the tool MatchTM to find potential binding sites in uncharacterized sequences, while PatchTM, another tool, uses the single sites (and IUPAC consensus sequences), which are stored in the SITE table. A new, third tool, P-MatchTM combines now the strengths of the matrix-based and the pattern-based approaches. While the binding sites are grouped into matrices to find a common denominator for the binding specificity of a certain factor, the transcription factors themselves are classified according to their DNA-binding domains in the CLASS table, as well as in a hierarchical factor classification tree. In addition to the binding properties of the transcription factors lots of information on their structure, function and tissue specificity is collected. In the GENE entries the respective sites and their binding factors, as well as the composite elements from TRANSCompel®, are summarized. As some of the regulated genes encode transcription factors themselves, there are not only links from factors via sites to target genes, but also from genes to encoded factors and vice versa. Based on these links "gene regulatory networks" can be retrieved/constructed. The GENE table does not only connect information of TRANSFAC® and TRANSCompel®, but also of other of our databases like HumanPSDTM, S/MARtDBTM, or TRANSPATH®, a database on signaling networks, into which the factor-site-gene interactions of TRANSFAC® are fully integrated. And finally, the GENE entries serve as major linking source to a growing number of (other) external databases. Public versions of TRANSFAC® and the above mentioned programs are freely accessible for research groups from non-profit organizations at http://www.gene-regulation.com. The professional version of TRANSFAC®, which contains not only a larger data amount but also an extended functionality, including integrated versions of Match® and Patch® as well as a tool for visualization of gene regulatory networks, is available at http://www.biobase-international.com.
Webpage:
http://www.gene-regulation.com/
Tags:
nucleic acid sequence transcription microarray data and other gene expression
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