De Novo Pathway Enrichment with KeyPathwayMiner

Nicolas Alcaraz; Anne Hartebrodt; Markus List

doi:10.1007/978-1-4939-9873-9_14

De Novo Pathway Enrichment with KeyPathwayMiner

Nicolas Alcaraz, Anne Hartebrodt, Markus List^*

^*Corresponding author for this work

Computational and RNA Biology

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 language	English
Title of host publication	Protein-Protein Interaction Networks : Methods and Protocols
Editors	Stefan Canzar, Francisca Rojas Ringeling
Number of pages	19
Publisher	Humana Press
Publication date	2020
Pages	181-199
Chapter	14
ISBN (Print)	978-1-4939-9872-2
ISBN (Electronic)	978-1-4939-9873-9
DOIs	https://doi.org/10.1007/978-1-4939-9873-9_14
Publication status	Published - 2020

Series	Methods in Molecular Biology
Volume	2074
ISSN	1064-3745

Keywords

Cytoscape
De novo pathway enrichment
Molecular interaction networks
Multi-omics

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10.1007/978-1-4939-9873-9_14

Cite this

De Novo Pathway Enrichment with KeyPathwayMiner. / Alcaraz, Nicolas; Hartebrodt, Anne; List, Markus.

Protein-Protein Interaction Networks: Methods and Protocols. ed. / Stefan Canzar; Francisca Rojas Ringeling. Humana Press, 2020. p. 181-199 (Methods in Molecular Biology, Vol. 2074).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

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De Novo Pathway Enrichment with KeyPathwayMiner

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Keywords

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