Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models. in a virulence factor of Xylella fastidiosa using a duplicated gene as a template. Nodes/spheres represent parent ions, and edge thickness corresponds to the cosine score. (2013) RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes. Since there is no cure, it has caused extreme devastation in southern Europe, especially in Apulia (Italy). Unfortunately, as mentioned above, there is also no cure for Xylella fastidiosa. The generated molecular network was imported and visualized as nodes and edges into Cytoscape 3.4.0 (Shannon et al., 2003). 7 reasons why Xylella fastidiosa is so dangerous. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. The spectra were also searched against GNPS’s spectral libraries, considering scores above 0.65 and at least four matched peaks. and PPPI network design was obtained using the Cytoscape software. Cytoscape's software Core provides basic functionality to layout and query the network to visually integrate the network with expression profiles, phenotypes, and other molecular states and to link the network to databases of functional annotations. The role of auxin in the citrus defense to early infection by Xylella fastidiosa. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework.
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