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De Novo Pathway Enrichment with KeyPathwayMiner

  • Nicolas Alcaraz
  • Anne Hartebrodt
  • Markus ListEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

De novo pathway enrichment Molecular interaction networks Cytoscape Multi-omics 

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Copyright information

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

Authors and Affiliations

  1. 1.Department of Biology, The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
  2. 2.TUM School of Life SciencesTechnical University of MunichFreisingGermany

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