Analyzing and interpreting genome data at the network level with ConsensusPathDB

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.

Outline of the protocol

rna-seq

Three paths of analysis are described in the protocol that depend on the user’s input. The content of the ConsensusPathDB (i.e., the integrated interaction graph and the predefined annotation sets) can be explored with single molecules (analysis path 1), with priority lists of molecules (genes, proteins and metabolites; analysis path 2) or with associated experimental data (analysis path 3). The Web server functionality includes over-representation analysis, enrichment analysis and network module analysis. The outputs are the generated tables and graphs that can be downloaded for further inspection.

Availability – ConsensusPathDB  is available at: http://consensuspathdb.org

Herwig R, Hardt C, Lienhard M, Kamburov A. (2016) Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat Protoc 11(10):1889-907. [abstract]

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