TRANSPATH ®—A High Quality Database Focused on Signal Transduction

Choi, Claudia; Krull, Mathias; Kel, Alexander; Kel-Margoulis, Olga; Pistor, Susanne; Potapov, Anatolij; Voss, Nico; Wingender, Edgar

TRANSPATH ®—A High Quality Database Focused on Signal Transduction

2004

Choi, Claudia(BIOBASE GmbH, Halchtersche Strasse 33) | Krull, Mathias(BIOBASE GmbH, Halchtersche Strasse 33) | Kel, Alexander(BIOBASE GmbH, Halchtersche Strasse 33) | Kel-Margoulis, Olga(BIOBASE GmbH, Halchtersche Strasse 33) | Pistor, Susanne(BIOBASE GmbH, Halchtersche Strasse 33) | Potapov, Anatolij(BIOBASE GmbH, Halchtersche Strasse 33) | Voss, Nico(BIOBASE GmbH, Halchtersche Strasse 33) | Wingender, Edgar(BIOBASE GmbH, Halchtersche Strasse 33)

TRANSPATH® can either be used as an encyclopedia, for both specific and generalinformation 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 manuallyextracted, mostly from the primary literature; the second is PathwayBuilder™,which provides several different types of network visualization and hence faciliatesunderstanding; the third is ArrayAnalyzer™, which is particularly suited to geneexpression array interpretation, and is able to identify key molecules within signallingnetworks (potential drug targets). These key molecules could be responsible forthe coordinated regulation of downstream events. Manual data extraction focuseson direct reactions between signalling molecules and the experimental evidence forthem, including species of genes/proteins used in individual experiments, experimentalsystems, materials and methods. This combination of materials and methods isused in TRANSPATH®to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen underphysiological conditions. Another important feature in TRANSPATH® is the inclusionof transcription factor–gene relations, which are transferred from TRANSFAC®,a database focused on transcription regulation and transcription factors. Sinceinteractions between molecules are mainly direct, this allows a complete andstepwise pathway reconstruction from ligands to regulated genes. More information isavailable at www.biobase.de/pages/products/databases.html.

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