ConsensusPathDB--a database for integrating human functional interaction networks

Abstract

ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26,133 distinct physical entities and 74,289 distinct functional interactions (protein-protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de.

Figure 1.

Graphical summary of the main functions of the ConsensusPathDB web interface. The search for interactions of specific entities or pathways, search for interaction paths, overrepresentation analysis and model upload induce specific interaction subnetworks that can be visualized in the dynamic visualization environment and exported in BioPAX format for further computational analysis, or as images. Different colors of nodes and edges refer to different types of interactions or entities and different source databases, respectively. The background image shows a screenshot of the ConsensusPathDB start page.

Figure 2.

Illustration of the mapping procedure. Two biochemical reactions that are identical according to their primary participants and the user-specified mapping criteria are mapped. The reaction A + B -> C + D, catalyzed by enzyme E1, originates from database X. A similar reaction, catalyzed by enzymes E1 and E2, originates from database Y. Since both reactions are identical according to the user-specified rules, the interactions are merged and visualized reflecting the source annotations.