Gene Expression Databases and Others

The control of protein synthesis has been an object of study since the middle of the last century. The initial analyses [16] showed the basic mechanisms of gene regulation in bacteria. Available databases concerning gene regulation and expression include TRANSFAC [17] and RegulonDB [18]. A limited version of TRANSFAC is available, and the professional version can be acquired with an academic license. RegulonDB contains data about bacteria and is freely available.

Our example handles regulatory mechanisms and gene expression processes. The simplified schema shown in Figure 11.6 is related to regulation in prokaryotes and contains ten classes that reference each other. Beginning at the class protein, for each protein the binding to enhancing and repressing binding sites is stored in interaction objects. An enhanced or repressed promoter controls transcription units (operons) containing a set of genes to be expressed. Final products of gene expression are polypeptides that function as either signals or enzymes. Sequence information can be used to predict hypothetical promoters and binding sites. Detailed information about the annotation of sequences in terms of genes and proteins can be gained from EMBL [19] and SwissProt [20].

The increasing number of databases requires efficient methods to access and integrate recent data mostly automatically. In addition, currently existing databases are growing rapidly, and integration methods have to be as generic as possible to be useful. Furthermore, molecular databases can be queried for information about static relationships between molecular objects. Obviously, the networks of objects created by

Fig. 11.6 Conceptual scheme of a gene regulatory database.

static relationships cannot be translated directly into mathematical models without additional modelling and mapping efforts.

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