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TRANSPATH®


NAR Molecular Biology Database Collection entry number 341
Krull, M.1, Pistor, S.1, Voss, N.1, Kel, A.1, Reuter, I.1, Potapov, A.1,2, Choi, C.1, Kel-Margoulis, O.1, Wingender, E.1,2
1BIOBASE GmbH, Halchtersche Strasse 33, D-38304 WolfenbÜttel, Germany
2Department of Bioinformatics, UKG, University of GÖttingen, Goldschmidtstrasse 1, D-37077 GÖttingen, Germany
Contact mkl@biobase.de

Database Description

TRANSPATH® is a database on signal transduction pathways that are modeled as bipartite graphs with molecules and reactions as node classes [1,2,3,4,5]. The molecule entries include polypeptides, modified forms, multicomponent complexes, high-order abstractions like families of proteins as well as other molecules such as Ca2+, NO, ATP, H2O. Reaction entries connect molecules, give information on the interaction mechanism and effects and constitute chains and pathways. Individual reactions or chains of subsequent reactions define a direction of signal flow [6]. The integration with TRANSFAC®, a database on transcription factors and their DNA binding sites [7], provides the possibility to present the complete signaling pathways, from extracellular ligands through adaptors and kinase cascades to transcription factors and their target genes. In many cases the protein products of target genes are themselves involved in signal transduction events. Data have been manually extracted from peer-reviewed literature and are curated by experts. The reliability of interaction data in terms of the biological relevance is evaluated and a respective quality value is assigned. Cross-references to important sequence and signature databases such as EMBL/GenBank, UniProt/Swiss-Prot, InterPro, or Ensembl, EntrezGene, RefSeq are provided. The database is equipped with the tools for data visualisation and analysis [1,2,4,5]. The PathwayBuilder™ tool offers four different modes of network visualisation.

Recent Developments

The molecule and reaction entries are hierarchically structured. Molecular components are present in several orthogonal hierarchies: according to species information, according to the modification status and organization in the complexes, and according to their function in the signaling flow. Reactions are described at three levels, molecular evidence, pathway steps and semantic. Individual signaling reactions with all mechanistic details available in the corresponding publication are stored at the molecular evidence level. The pathway steps have been presented in a form optimal for constructing the whole pathways; they are abstracted from species (within the mammalian or vertebrate taxon) still providing the mechanistic details. On the semantic level only those molecules are displayed that process and forward the signal. The current public release, TRANSPATH® 6.0, includes 20,155 molecules, 7,603 genes, 28,126 reactions. The professional releases of TRANSPATH®, equipped by the ArrayAnalyzer™ tool [2,5], are available at Biobase GmbH (www.biobase-international.com; info@biobase.de). The ArrayAnalyzer™ tool has been developed for the analysis of expression data. It serves to identify (potential) key nodes in the networks as well as to classify gene/protein lists according to TRANSPATH® pathways, GO terms, expression data, disease links.

Acknowledgements

Parts of the work were funded by grants of the German Ministry of Education and Research (BMBF) "Intergenomics" (031U210B), collectively by BioRegioN GmbH and BMBF "BioProfil" (0313092), by European Commission under FP6 "Life sciences, genomics and biotechnology for health" contract LSHG-CT-2004-503568 "COMBIO".

References

1. Schacherer,F., Choi,C., GÖtze,U., Krull,M., Pistor,S. and Wingender,E. (2001) The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics 17, 1053-1057.
2. Krull,M., Voss,N., Choi,C., Pistor,S., Potapov,A. and Wingender,E. (2003) TRANSPATH®: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res., 31, 97-100.
3. Wingender, E. (2003) TRANSFAC®, TRANSPATH® and CYTOMER® as starting points for an ontology of regulatory networks. In Silico Biol., 4, 0006.
4. Choi,C., Crass,T., Kel,A., Kel-Margoulis,O., Krull,M., Pistor,S., Potapov,A., Voss,N. and Wingender,E. (2004). Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform. Ser., 15, 244-254.
5. Kel-Margoulis,O., Matys,V., Choi,C., Reuter,I., Krull,M., Potapov,A.P., Voss,N., Liebich,I., Kel,A., and Wingender,E. (2005) Databases on Gene Regulation. In Bajic,V.B. and Tan,T.W. (ed.), Information Processing And Living Systems. World Scientific Publishing Co, Singapore, Vol. 2, pp. 709-727.
6. Potapov,A. and Wingender,E. (2001) Modeling the architecture of regulatory networks. In Wingender,E., HofestÄdt,R., Liebich,I. (eds.), Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig, pp. 6-10.
7. Matys,V., Fricke,E., Geffers,R., GÖßling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas, D., Kel,A.E., Kel-Margoulis,O.V., Kloos,D.U., Land,S., Lewicki-Potapov,B., Michael,H., MÜnch,R., Reuter,I., Rotert,S., Saxel,H., Scheer,M., Thiele,S., and Wingender,E. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.


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