However, Cytoscape is a general network tool, not a network database, and as such needs to import its networks from elsewhere. Moreover, Cytoscape has hundreds of apps, which users can install to add further functionality, such as clusterMaker2 4 that implements numerous clustering algorithms and PTMOracle 5 that allows PTMs to be analyzed in the context of protein networks. The Cytoscape software 2, 3, on the other hand, is designed to analyze and visualize very large networks and provides much greater flexibility in terms of import of additional data and visualization of these onto networks. However, the STRING web interface is not intended for large networks and provides limited flexibility in terms of network analysis and visualization, and accessing it without using the graphical user interface requires familiarity with programming. In addition to integrating available experimental data and pathways from curated databases, STRING predicts interactions based on co-expression analysis, evolutionary signals across genomes, automatic text-mining of the biomedical literature, and orthology-based transfer of evidence across organisms. The STRING database provides known and predicted protein–protein associations data for a large number of organisms, including both physical interactions and functional associations with confidence scores that quantify their reliability. Indeed, such networks are very frequently shown in proteomics publications. Protein network resources, in particular the STRING database 1, have proven highly useful for providing such context. Modern high-throughput technologies, including proteomics, produce an ever growing flow of new data on individual genes and proteins, which need to be interpreted in light of cellular context and existing biological knowledge. stringApp is freely available from the Cytoscape app store. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies.
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