@inbook{504940bdb81f48dd876727125f93fff0,
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",
year = "2020",
doi = "10.1007/978-1-4939-9873-9_14",
language = "English",
isbn = "978-1-4939-9872-2",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "181--199",
editor = "Stefan Canzar and Ringeling, {Francisca Rojas}",
booktitle = "Protein-Protein Interaction Networks",
address = "United States",
}