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De Novo Pathway Enrichment with KeyPathwayMiner

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Biomolecular networks such as protein–protein interaction networks provide a static picture of the interplay of genes and their products, and, consequently, they fail to capture dynamic changes taking place during the development of complex diseases. KeyPathwayMiner is a software platform designed to fill this gap by integrating previous knowledge captured in molecular interaction networks with OMICS datasets (DNA microarrays, RNA sequencing, genome-wide methylation studies, etc.) to extract connected subnetworks with a high number of deregulated genes. This protocol describes how to use KeyPathwayMiner for integrated analysis of multi-omics datasets in the network analysis tool Cytoscape and in a stand-alone web application available at https://keypathwayminer.compbio.sdu.dk.

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Author information

Authors and Affiliations

  1. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Nicolas Alcaraz

  2. TUM School of Life Sciences, Technical University of Munich, Freising, Germany

    Anne Hartebrodt & Markus List

Authors
  1. Nicolas Alcaraz
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  2. Anne Hartebrodt
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  3. Markus List
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Corresponding author

Correspondence to Markus List .

Editor information

Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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© 2020 Springer Science+Business Media, LLC, part of Springer Nature

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Alcaraz, N., Hartebrodt, A., List, M. (2020). De Novo Pathway Enrichment with KeyPathwayMiner. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_14

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_14

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

  • eBook Packages: Springer Protocols

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