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  Analyzing and interpreting genome data at the network level with ConsensusPathDB

Herwig, R., Hardt, C., Lienhard, M., & Kamburov, A. (2016). Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nature Protocols, 11(10), 1889-1907. doi:10.1038/nprot.2016.117.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002D-4779-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002D-477A-C
Genre: Journal Article

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© 2016 Macmillan Publishers Limited, part of Springer Nature
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Herwig, R.1, Author              
Hardt, C.1, Author              
Lienhard, M.1, Author              
Kamburov, A., Author
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385701              

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 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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Language(s): eng - English
 Dates: 2016-09-082016-10
 Publication Status: Published in print
 Pages: 19
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 Table of Contents: -
 Rev. Method: -
 Identifiers: PMID: 27606777
DOI: 10.1038/nprot.2016.117
ISSN: 1750-2799 (Electronic)
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Title: Nature Protocols
  Other : Nat. Protoc.
Source Genre: Journal
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Pages: - Volume / Issue: 11 (10) Sequence Number: - Start / End Page: 1889 - 1907 Identifier: ISSN: 1750-2799
CoNE: /journals/resource/1000000000223800_1