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Updated: Jan 26, 2026

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
Published on: August 21, 2019
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein
Bence Ágg1,2,3, Andrea Császár4, Máté Szalay-Bekő4,5
1Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1428 Budapest, Hungary.
Motivation:
Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules.
Results:
We present the EntOptLayout Cytoscape plug-in based on a recently developed network representation theory. The plug-in provides an efficient visualization of network modules, which represent major protein complexes in protein-protein interaction and signalling networks. Importantly, the tool gives a quality score of the network visualization by calculating the information loss between the input data and the visual representation showing a 3- to 25-fold improvement over conventional methods.
Availability And Implementation:
The plug-in (running on Windows, Linux, or Mac OS) and its tutorial (both in written and video forms) can be downloaded freely under the terms of the MIT license from: http://apps.cytoscape.org/apps/entoptlayout.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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