What is TRANSPATH® about?
TRANSPATH® is a database of mammalian signal transduction and metabolic pathways. As one of the earliest pathway databases ever created, it has grown since to the remarkable volume of more than 395,000 manually curated reactions. It is now an integral part of the BIOBASE Knowledge Library (BKL)/ PROTEOME Database, but can also be obtained as stand-alone product from geneXplain and as module of the geneXplain platform.
TRANSPATH organizes the information about genes/molecules and reactions according to multiple hierarchies. Its sophisticated structure makes it one of the scientifically best conceptualized pathway resources, suitable for multi-purpose uses. It is complemented by one of the richest corpora of pathway data available among all public domain and commercial sources, all manually curated by experts.
Complete networks and pathways are built from molecules and their reactions. To consider the heterogeneity of information given in the original publications, TRANSPATH transparently but precisely differentiates protein molecules according to:
Individual reactions are documented with all experimental details, in a strictly mechanistic way that includes all reaction partners and the taxonomic origin of each molecule as reported in the published experiment ("molecular evidence level"). All evidences for a certain pathway step are accumulated to provide a more comprehensive and complete picture ("pathway step level"). On top, a semantic view is provided, which focuses on the key components only and omits mechanistic details as well as small abundant molecules ("semantic projection").
Reaction hierarchy in the TRANSPATH® database on molecular pathways. (Click for an enlarged view.)
TRANSPATH key publications:
Wingender, E., Hogan, J., Schacherer, F., Potapov, A.P., Kel-Margoulis, O. (2007) Integrating pathway data for systems pathology. In Silico Biol. 7:S17-S25. PubMed.
Kel, A., Voss, N., Jauregui, R., Kel-Margoulis, O., Wingender, E. (2006) Beyond microarrays: find key transcription factors controlling signal transduction pathways. BMC Bioinformatics 7:S13. PubMed.
Krull, M., Pistor, S., Voss, N., Kel, A., Reuter, I., Kronenberg, D., Michael, H., Schwarzer, K., Potapov, A., Choi, C., Kel-Margoulis, O., Wingender, E. (2006) TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34:D546-D551. PubMed
Choi, C., Crass, T., Kel, A., Kel-Margoulis, O., Krull, M., Pistor, S., Potapov, A., Voss, N., Wingender, E. (2004) Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform. 15:244-254. PubMed
Choi, C., Krull, M., Kel, A., Kel-Margoulis, O., Pistor, S., Potapov, A., Voss, N., Wingender, E. (2004) TRANSPATH – a high quality database focused on signal transduction. Comp. Funct. Genomics 5:163-168. PubMed
Krull, M., Voss, N., Choi, C., Pistor, S., Potapov, A., Wingender, E. (2003) TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res. 31:97-100. PubMed
Schacherer, F., Choi, C., Götze, U., Krull, M., Pistor, S., Wingender, E. (2001) The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics 17:1053-1057. PubMed
Heinemeyer, T., Chen, X., Karas, H., Kel, A.E., Kel, O.V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F., Wingender, E. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res. 27:318-322. PubMed