![]() ![]() This feature facilitates the integration of our software with other tools available in the Cytoscape platform. Cytoscape is one of the most widespread software platforms for visualizing and integrating network data. In addition, an option is provided to allow other networks to be converted to BisoGenet. Several tools as Cytoscape14,15, VisANT, Osprey and Biological Networks, have being developed for reconstruction and visualization of networks of biological entities, for reviews see Pavlopoulos et al. The MCODE algorithm, one of the Cytoscape plugins, was used to identify highly interconnected sub-networks with parameter settings, including Degree Cutoff2, Node Score Cutoff0. The client application includes network analysis tools and interactive network expansion capabilities. The STRING and Bisogenet PPI (HPRD database) networks were merged, and the resulted network was used to identify clusters using the MCODE Plug-in. This feature could be instrumental to achieve a finer grain representation of the bioentities and their relationships. A feature of Bisogenet is the possibility to include coding relations to distinguish between genes and their products. BisoGenet also includes network topology analysis tools such as Shortest Paths between a set of nodes, determination of Equivalent Nodes, and Network Statistics reports in combination to interactive Transparency filter to help discernig such analytical results in the context of dense networks. The interactions between active compounds and hub genes were revealed by molecular docking. GO and KEGG analyses were performed by the DAVID online tool. Conclusion BisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. The compound-target and protein-protein interaction networks were constructed by Cytoscape 3.8 and BisoGenet, respectively. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network.īisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network. In the middle tier, a global network is created at server startup, representing the whole data on bioentities and their relationships retrieved from the database. In the data tier, an in-house database stores genomics information, protein-protein interactions, protein-DNA interactions, gene ontology and metabolic pathways. The development of software tools capable of integrating data from different sources and to provide flexible methods to reconstruct, represent and analyze topological networks is an active field of research in bioinformatics.īisoGenet is a multi-tier application for visualization and analysis of biomolecular relationships. Graph-based biological networks models capture the topology of the functional relationships between molecular entities such as gene, protein and small compounds and provide a suitable framework for integrating and analyzing omics-data. The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. ![]()
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