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Media type:
E-Article
Title:
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein–protein interaction and signalling networks
Contributor:
Ágg, Bence;
Császár, Andrea;
Szalay-Bekő, Máté;
Veres, Dániel V;
Mizsei, Réka;
Ferdinandy, Péter;
Csermely, Péter;
Kovács, István A
Description:
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>Network visualizations of complex biological datasets usually result in ‘hairball’ images, which do not discriminate network modules.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>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.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>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.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
</jats:sec>