CytoGEDEVO-global alignment of biological networks with Cytoscape

Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach

Research output: Contribution to journalArticleResearchpeer-review

Abstract

MOTIVATION: In the systems biology era, high-throughput omics technologies have enabled the unraveling of the interplay of some biological entities on a large scale (e.g. genes, proteins, metabolites or RNAs). Huge biological networks have emerged, where nodes correspond to these entities and edges between them model their relations. Protein-protein interaction networks, for instance, show the physical interactions of proteins in an organism. The comparison of such networks promises additional insights into protein and cell function as well as knowledge-transfer across species. Several computational approaches have been developed previously to solve the network alignment (NA) problem, but only a few concentrate on the usability of the implemented tools for the evaluation of protein-protein interactions by the end users (biologists and medical researchers).

RESULTS: We have created CytoGEDEVO, a Cytoscape app for visual and user-assisted NA. It extends the previous GEDEVO methodology for global pairwise NAs with new graphical and functional features. Our main focus was on the usability, even by non-programmers and the interpretability of the NA results with Cytoscape.

AVAILABILITY AND IMPLEMENTATION: CytoGEDEVO is publicly available from the Cytoscape app store at http://apps.cytoscape.org/apps/cytogedevo In addition, we provide stand-alone command line executables, source code, documentation and step-by-step user instructions at http://cytogedevo.compbio.sdu.dk

CONTACT: malek@tugraz.at

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)1259-61
Number of pages3
JournalBioinformatics
Volume32
Issue number8
DOIs
Publication statusPublished - 15 Apr 2016

Fingerprint

Biological Networks
Alignment
Proteins
Application programs
Protein-protein Interaction
Protein
Usability
Knowledge Transfer
Protein Interaction Networks
Interpretability
Systems Biology
High Throughput
Protein Interaction Maps
Pairwise
Bioinformatics
Availability
Gene
Computational Biology
Documentation
Metabolites

Keywords

  • Computational Biology/methods
  • Programming Languages
  • Protein Interaction Maps
  • Proteins
  • Software
  • Systems Biology

ASJC Scopus subject areas

  • Computer Science Applications

Fields of Expertise

  • Information, Communication & Computing
  • Human- & Biotechnology

Treatment code (Nähere Zuordnung)

  • Application

Cite this

CytoGEDEVO-global alignment of biological networks with Cytoscape. / Malek, Maximilian; Ibragimov, Rashid; Albrecht, Mario; Baumbach, Jan.

In: Bioinformatics, Vol. 32, No. 8, 15.04.2016, p. 1259-61.

Research output: Contribution to journalArticleResearchpeer-review

Malek, Maximilian ; Ibragimov, Rashid ; Albrecht, Mario ; Baumbach, Jan. / CytoGEDEVO-global alignment of biological networks with Cytoscape. In: Bioinformatics. 2016 ; Vol. 32, No. 8. pp. 1259-61.
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N2 - MOTIVATION: In the systems biology era, high-throughput omics technologies have enabled the unraveling of the interplay of some biological entities on a large scale (e.g. genes, proteins, metabolites or RNAs). Huge biological networks have emerged, where nodes correspond to these entities and edges between them model their relations. Protein-protein interaction networks, for instance, show the physical interactions of proteins in an organism. The comparison of such networks promises additional insights into protein and cell function as well as knowledge-transfer across species. Several computational approaches have been developed previously to solve the network alignment (NA) problem, but only a few concentrate on the usability of the implemented tools for the evaluation of protein-protein interactions by the end users (biologists and medical researchers).RESULTS: We have created CytoGEDEVO, a Cytoscape app for visual and user-assisted NA. It extends the previous GEDEVO methodology for global pairwise NAs with new graphical and functional features. Our main focus was on the usability, even by non-programmers and the interpretability of the NA results with Cytoscape.AVAILABILITY AND IMPLEMENTATION: CytoGEDEVO is publicly available from the Cytoscape app store at http://apps.cytoscape.org/apps/cytogedevo In addition, we provide stand-alone command line executables, source code, documentation and step-by-step user instructions at http://cytogedevo.compbio.sdu.dkCONTACT: malek@tugraz.atSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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