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.


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:

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*


  • Proteins