TRANSPATH®

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.

Webpage:
http://www.gene-regulation.com/pub/databases.html#transpath

Tags:

nucleic acid sequence transcription metabolic and signaling pathways protein-protein interactions

More to explore:

1/20

Previous Next   



Need help integrating and/or managing biomedical data?