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Analyzing and interpreting genome data at the network level with ConsensusPathDB

Abstract

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 (http://consensuspathdb.org) 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.

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Figure 1: Outline of the protocol.
Figure 2: Pathways and interactions in ConsensusPathDB.
Figure 3: Interaction neighborhood retrieval in ConsensusPathDB.
Figure 4: Over-representation analysis with gene lists in ConsensusPathDB.
Figure 5: Over-representation analysis with list of metabolites in ConsensusPathDB.
Figure 6: Induced network module analysis in ConsensusPathDB.
Figure 7: Enrichment analysis with RNA-seq data in ConsensusPathDB.

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Acknowledgements

We are grateful to all scientists who provided annotation of the original molecular interaction data and are allowing automated access to their databases. Integration of interaction data could be achieved only because the original data were provided in an excellently documented way.

This work was financed in part by the European Commission under its 7th Framework Programme (HeCaToS 602156 to R.H.) and the Max Planck Society.

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Authors and Affiliations

Authors

Contributions

R.H. and A.K. conceived ConsensusPathDB, designed the protocol and wrote the manuscript; A.K. developed ConsensusPathDB; C.H. and M.L. conducted the procedure, performed data analysis and contributed to the manuscript.

Corresponding authors

Correspondence to Ralf Herwig or Atanas Kamburov.

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Competing interests

The authors declare no competing financial interests.

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Herwig, R., Hardt, C., Lienhard, M. et al. Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat Protoc 11, 1889–1907 (2016). https://doi.org/10.1038/nprot.2016.117

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