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

Research output: Contribution to journalArticle

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 languageEnglish
Pages (from-to)4490-4492
Number of pages3
JournalBioinformatics
Volume35
Issue number21
DOIs
Publication statusPublished - Nov 1 2019

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Protein Interaction Maps
Protein-protein Interaction
Plug-in
Visualization
Proteins
Protein
Application programs
Licensure
Availability
Module
Information Loss
Linux
Representation Theory
Fold
Term
Datasets

ASJC Scopus subject areas

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

Cite this

The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks. / Ágg, Bence; Császár, Andrea; Szalay-Beko, Máté; Veres, Dániel V.; Mizsei, Réka; Ferdinandy, Péter; Csermely, Péter; Kovács, István A.

In: Bioinformatics, Vol. 35, No. 21, 01.11.2019, p. 4490-4492.

Research output: Contribution to journalArticle

Ágg, Bence ; Császár, Andrea ; Szalay-Beko, Máté ; Veres, Dániel V. ; Mizsei, Réka ; Ferdinandy, Péter ; Csermely, Péter ; Kovács, István A. / The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks. In: Bioinformatics. 2019 ; Vol. 35, No. 21. pp. 4490-4492.
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AU - Mizsei, Réka

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