Orthoscape: A cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles

Zakhar Sergeevich Mustafin, Sergey Alexandrovich Lashin, Yury Georgievich Matushkin, Konstantin Vladimirovich Gunbin, Dmitry Arkadievich Afonnikov

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

Abstract

Background: There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Results: Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Conclusion: Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

Original languageEnglish
Article number28
Pages (from-to)1427
Number of pages9
JournalBioinformatics
Volume18
Issue numberSuppl 1
DOIs
Publication statusPublished - 27 Jan 2017

Keywords

  • Cytoscape plugin
  • Evolution
  • Gene regulatory network
  • Metabolic pathway
  • Ortholog
  • Paralog
  • Phylostratigraphy
  • Humans
  • Databases, Genetic
  • Computational Biology/methods
  • Gene Regulatory Networks
  • Sequence Homology, Nucleic Acid
  • Computer Graphics
  • Software
  • Evolution, Molecular
  • STEROIDS
  • ADAPTATION
  • SEQUENCE
  • IDENTIFICATION
  • SOFTWARE
  • PROTEIN-INTERACTION NETWORKS
  • EVOLUTION
  • BIOLOGICAL NETWORKS
  • INTEGRATION
  • TOOL

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