De Novo Pathway Enrichment with KeyPathwayMiner

Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt

Standard

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

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

Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt

Harvard

Alcaraz, N, Hartebrodt, A & List, M 2020, De Novo Pathway Enrichment with KeyPathwayMiner. i S Canzar & FR Ringeling (red), Protein-Protein Interaction Networks: Methods and Protocols. Humana Press, Methods in Molecular Biology, bind 2074, s. 181-199. https://doi.org/10.1007/978-1-4939-9873-9_14

APA

Alcaraz, N., Hartebrodt, A., & List, M. (2020). De Novo Pathway Enrichment with KeyPathwayMiner. I S. Canzar, & F. R. Ringeling (red.), Protein-Protein Interaction Networks: Methods and Protocols (s. 181-199). Humana Press. Methods in Molecular Biology Bind 2074 https://doi.org/10.1007/978-1-4939-9873-9_14

Vancouver

Alcaraz N, Hartebrodt A, List M. De Novo Pathway Enrichment with KeyPathwayMiner. I Canzar S, Ringeling FR, red., Protein-Protein Interaction Networks: Methods and Protocols. Humana Press. 2020. s. 181-199. (Methods in Molecular Biology, Bind 2074). https://doi.org/10.1007/978-1-4939-9873-9_14

Author

Alcaraz, Nicolas ; Hartebrodt, Anne ; List, Markus. / De Novo Pathway Enrichment with KeyPathwayMiner. Protein-Protein Interaction Networks: Methods and Protocols. red. / Stefan Canzar ; Francisca Rojas Ringeling. Humana Press, 2020. s. 181-199 (Methods in Molecular Biology, Bind 2074).

Bibtex

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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",

}

RIS

TY - CHAP

T1 - De Novo Pathway Enrichment with KeyPathwayMiner

AU - Alcaraz, Nicolas

AU - Hartebrodt, Anne

AU - List, Markus

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

KW - Cytoscape

KW - De novo pathway enrichment

KW - Molecular interaction networks

KW - Multi-omics

U2 - 10.1007/978-1-4939-9873-9_14

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

M3 - Book chapter

C2 - 31583639

AN - SCOPUS:85072910199

SN - 978-1-4939-9872-2

T3 - Methods in Molecular Biology

SP - 181

EP - 199

BT - Protein-Protein Interaction Networks

A2 - Canzar, Stefan

A2 - Ringeling, Francisca Rojas

PB - Humana Press

ER -

ID: 230742618