TRANSPATH® release 2021.1
The TRANSPATH® database on mammalian signal transduction and metabolic pathways contains these new data features:
- New pathway visualization
The pathway visualization tool was completely re-developed into a new PathFinder perspective of the geneXplain bioinformatics platform. It supports SBGN and SBML standards and details the location of molecules in the main intracellular compartments at a significantly improved performance.
- Increase in number of reactions
3,881 new binding reactions between proteins in human have been added, among them e.g. from the MAP4K interactome and the Ras interactome.
- Update of links to pathway databases
Links from genes/proteins to the pathway databases Reactome (version 75) and Wikipathways (20201110) have been updated.
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