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 data are available at Bioinformatics online. Contact: [email protected]
Cite
@article{arxiv.1904.03910,
title = {The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks},
author = {Bence Agg and Andrea Csaszar and Mate Szalay-Beko and Daniel V. Veres and Reka Mizsei and Peter Ferdinandy and Peter Csermely and Istvan A. Kovacs},
journal= {arXiv preprint arXiv:1904.03910},
year = {2019}
}