Abstract
BackgroundThere 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.ResultsOrthoscape 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.ConclusionOrthoscape 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.
Highlights
There are many available software tools for visualization and analysis of biological networks
[18,19,20], signaling [21, 22] as well as ecological-type networks including food webs, communities network and others. In spite of such great diversity, evolutionoriented plugins are in short supply: just three plugins tagged ‘network evolution’ in Cytoscape official app store and in literature
Number of tools have been developed to operate with KEGG pathway maps including CyKEGGParser [27], ANIMO [28] and SIREN [16]
Summary
There are many available software tools for visualization and analysis of biological networks. [18,19,20], signaling [21, 22] as well as ecological-type networks including food webs, communities network and others In spite of such great diversity, evolutionoriented plugins are in short supply: just three plugins tagged ‘network evolution’ (even not ‘biological evolution’) in Cytoscape official app store and in literature. These include ANIMO [23], TieDIE, NetworkEvolution [24]) and a couple of plugins concerning orthology analysis (HOMECAT [25] and OrthoNets [26]). Number of tools have been developed to operate with KEGG pathway maps including CyKEGGParser [27], ANIMO [28] and SIREN [16]
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