The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks
This tool addresses visualization challenges for researchers analyzing protein-protein interaction and signalling networks, but it is incremental as it builds on existing network representation theory.
The authors tackled the problem of 'hairball' network visualizations in biological datasets by developing the EntOptLayout Cytoscape plug-in, which efficiently visualizes network modules representing major protein complexes and shows a 3- to 25-fold improvement in quality score over conventional methods.
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: csermely.peter@med.semmelweis-univ.hu