Integration of biological networks and gene expression data using Cytoscape
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5,569 citations
Cites methods from "Integration of biological networks ..."
...To bridge the gap between the two, we have developed a so-called App for the Cytoscape software framework (44,45), which allows users to easily retrieve, visualize and analyze networks of hundreds to thousands of proteins via a GUI....
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4,919 citations
Cites methods from "Integration of biological networks ..."
...For data visualization, REVIGO relies on Google Motion Chart for scatterplots, Cytoscape Web [12] for graphs and DrasticTreemap for treemaps....
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...The placement of the nodes is determined by the ForceDirected layout algorithm as implemented in Cytoscape Web [12]....
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...Any modern internet browser with Adobe Flash capabilities is sufficient to access the server; additionaly, client-side Java is required if Cytoscape [13] is invoked via Java Web Start....
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...Tool Brief description BINGO [21] Cytoscape plug-in that tests for GO category enrichment in a list or network of genes, and displays the results in a graph of GO terms....
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...In addition to being viewed in the Web browser, the graph may be exported to a XGMML file, or opened in the standalone Cytoscape program [13] via Java Web Start to produce high resolution, publication-quality images....
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4,722 citations
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4,186 citations
3,239 citations
Cites methods from "Integration of biological networks ..."
...Cytoscape is a widely used open-source software framework for network visualization and manipulation (54,55); it can be very flexibly extended, with a rapidly growing number of network-centered manipulation and analysis tools....
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References
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