TY - JOUR

T1 - Orthoscape

T2 - A cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles

AU - Mustafin, Zakhar Sergeevich

AU - Lashin, Sergey Alexandrovich

AU - Matushkin, Yury Georgievich

AU - Gunbin, Konstantin Vladimirovich

AU - Afonnikov, Dmitry Arkadievich

N1 - Publisher Copyright: © 2017 The Author(s).

PY - 2017/1/27

Y1 - 2017/1/27

N2 - 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.

AB - 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.

KW - Cytoscape plugin

KW - Evolution

KW - Gene regulatory network

KW - Metabolic pathway

KW - Ortholog

KW - Paralog

KW - Phylostratigraphy

KW - Humans

KW - Databases, Genetic

KW - Computational Biology/methods

KW - Gene Regulatory Networks

KW - Sequence Homology, Nucleic Acid

KW - Computer Graphics

KW - Software

KW - Evolution, Molecular

KW - STEROIDS

KW - ADAPTATION

KW - SEQUENCE

KW - IDENTIFICATION

KW - SOFTWARE

KW - PROTEIN-INTERACTION NETWORKS

KW - EVOLUTION

KW - BIOLOGICAL NETWORKS

KW - INTEGRATION

KW - TOOL

UR - http://www.scopus.com/inward/record.url?scp=85013789352&partnerID=8YFLogxK

U2 - 10.1186/s12859-016-1427-5

DO - 10.1186/s12859-016-1427-5

M3 - Article

C2 - 28466792

AN - SCOPUS:85013789352

VL - 18

SP - 1

EP - 9

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - Suppl 1

M1 - 28

ER -