The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

Bence Ágg; Andrea Császár; Máté Szalay-Bekő; Dániel V Veres; Réka Mizsei; Péter Ferdinandy; Péter Csermely; István A Kovács

doi:10.1093/bioinformatics/btz257

The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

Bioinformatics. 2019 Nov 1;35(21):4490-4492. doi: 10.1093/bioinformatics/btz257.

Authors

Bence Ágg^{1

2

3}, Andrea Császár⁴, Máté Szalay-Bekő^{4

5}, Dániel V Veres^{4

6}, Réka Mizsei⁷, Péter Ferdinandy^{1

3}, Péter Csermely⁴, István A Kovács^{8

9

10}

Affiliations

¹ Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1428 Budapest, Hungary.
² Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary.
³ Pharmahungary Group, 6722 Szeged, Hungary.
⁴ Department of Medical Chemistry, Semmelweis University, 1428 Budapest, Hungary.
⁵ Earlham Institute Norwich Research Park, Norwich NR4 7UZ, UK.
⁶ Turbine Ltd, 1136 Budapest, Hungary.
⁷ Laboratory of Immunobiology, Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
⁸ Network Science Institute, Northeastern University, Boston, MA 02115, USA.
⁹ Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
¹⁰ Wigner Research Centre for Physics, Institute for Solid State Physics and Optics, 1525 Budapest, Hungary.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Computational Biology
Protein Binding
Proteins
Signal Transduction
Software*

Substances

Proteins