Research output: Contribution to journal › Article › peer-review
Orthoscape : A cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. / Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich et al.
In: Bioinformatics, Vol. 18, No. Suppl 1, 28, 27.01.2017, p. 1-9.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 10306095