ConsensusPathDB data access

Data download

Protein interaction network in tab-delimited format
Protein interaction network in PSI-MI (level 2.5) format

The protein interaction part of the integrated network is available for download. Due to several licensing issues, we are not allowed to release the complete integrated network (including signaling, metabolism and gene regulation).
Rows with one protein only describe self-interactions, and rows with more than two proteins describe complex interactions. In cases when proteins are annotated only with genomic identifiers but no protein identifiers in the according source databases, and if the genomic identifiers map to more than one UniProt entry, the according UniProt entry names are concatenated (e.g. RL40_HUMAN.RS27A_HUMAN.UBIQ_HUMAN) as it is unclear which of the gene products interact.

Biological pathways (as defined by source databases) with their genes identified with accession numbers
Biological pathways (as defined by source databases) with their metabolites identified with KEGG / ChEBI / Pubchem-compound accession numbers

ConsensusPathDB plugin for Cytoscape

With the ConsensusPathDB plugin for Cytoscape you can mine evidence (publications, detection methods, pathways, etc.) for interactions loaded in Cytoscape and highlight interactions that have not been detected previously. Please read our paper on the plugin to learn how to use it.

Web services

Automated access to ConsensusPathDB's over-representation and enrichment analysis functionality is possible through a SOAP/WSDL interface.
The WSDL file needed for connecting to the SOAP/WSDL interface is located at Each function is documented in the WSDL file. An example Python client is avilable here.