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-Beko; 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

Bence Ágg, Andrea Császár, Máté Szalay-Beko, Dániel V. Veres, Réka Mizsei, Péter Ferdinandy, Péter Csermely^*, István A. Kovács

^*Corresponding author for this work

Physics and Astronomy

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

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.

Original language	English (US)
Pages (from-to)	4490-4492
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btz257
State	Published - Nov 1 2019

ASJC Scopus subject areas

Computational Mathematics
Molecular Biology
Biochemistry
Statistics and Probability
Computer Science Applications
Computational Theory and Mathematics

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10.1093/bioinformatics/btz257

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

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.",

author = "Bence {\'A}gg and Andrea Cs{\'a}sz{\'a}r and M{\'a}t{\'e} Szalay-Beko and Veres, {D{\'a}niel V.} and R{\'e}ka Mizsei and P{\'e}ter Ferdinandy and P{\'e}ter Csermely and Kov{\'a}cs, {Istv{\'a}n A.}",

note = "Funding Information: This work was supported by the Hungarian National Research, Development and Innovation Office (Grant Nos. NVKP_16-1-2016-0017, B.{\'A}.; KH_17-125570, P.F. and K115378, P.C.) and by the Higher Education Institutional Excellence Programme of the Ministry of Human Capacities in Hungary, within the framework of the Therapeutic Development (P.F.) and Molecular Biology (P.C.) thematic programmes of the Semmelweis University. Publisher Copyright: {\textcopyright} The Author(s) 2019. Published by Oxford University Press.",

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doi = "10.1093/bioinformatics/btz257",

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T1 - The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks

AU - Ágg, Bence

AU - Császár, Andrea

AU - Szalay-Beko, Máté

AU - Veres, Dániel V.

AU - Mizsei, Réka

AU - Ferdinandy, Péter

AU - Csermely, Péter

AU - Kovács, István A.

N1 - Funding Information: This work was supported by the Hungarian National Research, Development and Innovation Office (Grant Nos. NVKP_16-1-2016-0017, B.Á.; KH_17-125570, P.F. and K115378, P.C.) and by the Higher Education Institutional Excellence Programme of the Ministry of Human Capacities in Hungary, within the framework of the Therapeutic Development (P.F.) and Molecular Biology (P.C.) thematic programmes of the Semmelweis University. Publisher Copyright: © The Author(s) 2019. Published by Oxford University Press.

PY - 2019/11/1

Y1 - 2019/11/1

N2 - 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.

AB - 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.

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

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