The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3-D cell

Yose Y. Widjaja, Chi Nam Ignatius Pang, Simone S. Li, Marc R. Wilkins, Tim D. Lambert

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

Abstract

Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.

Original languageEnglish
Pages (from-to)5309-5315
Number of pages7
JournalProteomics
Volume9
Issue number23
DOIs
Publication statusPublished - Dec 2009
Externally publishedYes

Keywords

  • Complexome
  • Networks
  • Protein-protein interactions
  • Systems biology
  • Virtual cell

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