Analyzing and interpreting genome data at the network level with ConsensusPathDB

Nat Protoc. 2016 Oct;11(10):1889-907. doi: 10.1038/nprot.2016.117. Epub 2016 Sep 8.


ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB ( with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Databases, Genetic
  • Gene Ontology
  • Genome
  • Genomics / methods*
  • Humans
  • Internet
  • Metabolic Networks and Pathways*
  • Metabolomics / methods
  • Mice
  • Protein Interaction Maps*
  • Proteins / genetics*
  • Proteins / metabolism*
  • Software
  • User-Computer Interface
  • Yeasts


  • Proteins