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

Research output: Contribution to journalArticle

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

ASJC Scopus subject areas

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

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