@inbook{9cc63674ffe24ab298ec9299a0097a10,
title = "De novo pathway enrichment with keypathwayminer",
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.",
keywords = "Cytoscape, De novo pathway enrichment, Molecular interaction networks, Multi-omics",
author = "Nicolas Alcaraz and Anne Hartebrodt and Markus List",
note = "Publisher Copyright: {\textcopyright} Springer Science+Business Media, LLC, part of Springer Nature 2020.",
year = "2020",
doi = "10.1007/978-1-4939-9873-9\_14",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "181--199",
booktitle = "Methods in Molecular Biology",
}