Pathways / Hypergeometric test for ConsensusPathDB


Searches gene lists for over-represented pathways in the ConsensusPathDB (CPDB). This service is provided by the Max Planck Institute for Molecular Genetics.



This tool takes a filtered data set (e.g. a list of differentially expressed genes) and goes through all the pathways in CPDB. CPDB is a database that integrates pathway and other functional interaction resources like Reactome, HumanCyc, BioCarta, Pathway Interaction Database and others. For every pathway, a hypergeometric test is calculated, and the pathways that acquire a p-value smaller than the user-specified threshold are reported. This tool works with human, mouse and yeast data containing gene symbols or UniProt identifiers. The background size used in the p-value calculation is the number of CPDB entities annotated with the corresponding identifiers (UniProt or gene symbols).


Result files include a list of significant pathways as text file (allows sorting by columns) and as an html file (with hyperlinks to the corresponding entries in the CPDB member databases). In addition the mappings of the significant pathways are added to the input list of genes/proteins.


More information can be found at the CPDB website and in the following article:

Kamburov et al: ConsensusPathDB interaction database: 2013 update. Nuc Acids Res 41:793-800 (2013)