De novo pathway enrichment with keypathwayminer

Nicolas Alcaraz, Anne Hartebrodt, Markus List

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

3 Scopus citations

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages181-199
Number of pages19
DOIs
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
Volume2074
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Cytoscape
  • De novo pathway enrichment
  • Molecular interaction networks
  • Multi-omics

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