TRANSPATH

 

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 458,000 manually curated reactions. One of the largest pathway databases available, optimally suited for geneXplain’s proprietary Upstream Analysis

Its contents can be used for pathway analysis with the geneXplain platform, requiring separate licensing (see below).

Structure

Reaction hierarchy in the TRANSPATH® database of molecular pathways.

Reaction hierarchy in the TRANSPATH® database on molecular pathways. (Click image for an enlarged view.)

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.

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”).

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:

  • their relatedness within one genome
    Information can be specifically retrieved regarding

    • (a) specific individual proteins,
    • (b) all products of a certain gene (isoforms),
    • (c) different family relation levels (e.g., paralogs);
  • their relatedness between different genomes (orthology)
  • their association and modification status
    • (a) protein complexes are specified with their exact composition;
    • (b) post-translational modifications are given with their exact positions in the protein.

TGFbeta network

Visualization of a part of the TGFbeta network with the geneXplain platform; data were retrieved from the TRANSPATH® database. The one molecule of the displayed network that is not genome-encoded (PtdIns(3)P), phosphatidylinositol 3-phosphate) is shown in purple.

Visualization of the TGFbeta network with the geneXplain platform; data were retrieved from the TRANSPATH® database. (Click image to enlarge the picture.)

Key features

Information about more than 298,000 molecules and more than 80,000 genes involved in signaling or metabolic pathways of mammals (mostly human, mouse, rat), gathered by manual expert curation.
More than 489,000 reactions extracted from original scientific literature and evaluated by experts.
About 1720 experimentally verified pathways and chains.
More than 98,000 transcription factor – site interactions, manually annotated and quality-checked.
More than 60,000 peer-reviewed scientific publications evaluated.
Highly customizable view of pathways and networks under the geneXplain platform.

Benefits

Quickly access information about signal transduction and metabolic pathway components and their reactions without tedious and time consuming literature searches.

Predict potential pathways targeting the genes of your interest.

Build customized regulatory and metabolic networks.

Use advanced TRANSPATH®-based network visualization technology of the geneXplain platform.

Pathway analysis

Get a picture of TRANSPATH®

Pathway analysis and network visualization with the geneXplain platform using the TRANSPATH® database.

Pathway analysis and network visualization with the geneXplain platform using the TRANSPATH® database. (Click image to enlarge the picture.)

Learn more about pathway analysis with the geneXplain platform.

Current TRANSPATH® release

TRANSPATH® release 2020.3

The TRANSPATH® database on mammalian signal transduction and metabolic pathways contains these new data features:

  • Increase in number of reactions

15,202 new binding reactions between proteins in human have been added, among them e.g. from the IFN-beta stimulated and unstimulated interactome or the beta-actin interactome.

  • Interactions between SARS-CoV-2 and human proteins

For 26 SARS-CoV-2 proteins, 330 interactions with protein targets in human cells were imported (Gordon, D. E. et al., Nature 583, 459-468 (2020), Pubmed 32353859).

  • Update of links to pathway databases

Links from genes/proteins to the pathway databases Reactome (version 73) and Wikipathways (20200710) have been updated. Wikipathways links now also include zebra fish (Danio rerio) and SARS-CoV-2 related pathways.

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    TRANSPATH applications

    Information downloads

    TRANSPATH® Statistics (download)
    TRANSPATH® Features (download)
    TRANSPATH® Flyer (download)
    TRANSPATH® Documentation (download)
    Sample flat file for 3 molecule entries (download)
    Sample flat file for 4 reaction entries (download)
    Sample flat file for 2 pathway entries (download)
    TRANSPATH® is a registered trademark of QIAGEN.

    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

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