<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>TRANSPATH<sup>®</sup>
can either be used as an encyclopedia, for both specific and general
information on signal transduction, or can serve as a network analyser. Therefore,
three modules have been created: the first one is the data, which have been manually
extracted, mostly from the primary literature; the second is PathwayBuilder<sup>™</sup>,
which provides several different types of network visualization and hence faciliates
understanding; the third is ArrayAnalyzer<sup>™</sup>, which is particularly suited to gene
expression array interpretation, and is able to identify key molecules within signalling
networks (potential drug targets). These key molecules could be responsible for
the coordinated regulation of downstream events. Manual data extraction focuses
on direct reactions between signalling molecules and the experimental evidence for
them, including species of genes/proteins used in individual experiments, experimental
systems, materials and methods. This combination of materials and methods is
used in TRANSPATH<sup>®</sup>
to assign a quality value to each experimentally proven reaction, 
which reflects the probability that this reaction would happen under
physiological conditions. Another important feature in TRANSPATH<sup>®</sup> is the inclusion
of transcription factor–gene relations, which are transferred from TRANSFAC<sup>®</sup>,
a database focused on transcription regulation and transcription factors. Since
interactions between molecules are mainly direct, this allows a complete and
stepwise pathway reconstruction from ligands to regulated genes. More information is
available at www.biobase.de/pages/products/databases.html.</p>
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Comp Funct Genomics. 2004 Mar; 5(2):163-168