eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

Mohammed El-Kebir; Philipp Spohr; Kasper Dinkla; Gunnar W. Klau

doi:10.12688/f1000research.14612.1

eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

Mohammed El-Kebir, Philipp Spohr, Kasper Dinkla, Gunnar W. Klau

Research output: Contribution to journal › Article › peer-review

Abstract

eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs.

Original language	English (US)
Article number	519
Journal	F1000Research
Volume	7
DOIs	https://doi.org/10.12688/f1000research.14612.1
State	Published - 2018

Keywords

Enrichment
Euler diagram
Functional subnetwork modules
Graph drawing
Network community
Visualization

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)
Pharmacology, Toxicology and Pharmaceutics(all)

Online availability

10.12688/f1000research.14612.1

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title = "eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]",

abstract = "eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs.",

keywords = "Enrichment, Euler diagram, Functional subnetwork modules, Graph drawing, Network community, Visualization",

author = "Mohammed El-Kebir and Philipp Spohr and Kasper Dinkla and Klau, {Gunnar W.}",

note = "Publisher Copyright: {\textcopyright} 2018 Spohr P et al.",

year = "2018",

doi = "10.12688/f1000research.14612.1",

language = "English (US)",

volume = "7",

journal = "F1000Research",

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T2 - Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

AU - El-Kebir, Mohammed

AU - Spohr, Philipp

AU - Dinkla, Kasper

AU - Klau, Gunnar W.

PY - 2018

Y1 - 2018

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AB - eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs.

KW - Enrichment

KW - Euler diagram

KW - Functional subnetwork modules

KW - Graph drawing

KW - Network community

KW - Visualization

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eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

Abstract

Keywords

ASJC Scopus subject areas

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