USING CYTOSCAPE INSTALL
Note that you need to install the app for the charts to show. The app provides several different types of charts to show the enriched terms. In addition, *stringApp* can retrieve functional enrichment for Gene Ontology terms, KEGG, Reactome and Wiki Pathways, DISEASES, COMPARTMENTS, TISSUES, and protein domains at a user-specified significance threshold and show the results in a new table in the Table Panel. All STRING networks are visualized using a new "String Style" custom graphic, which closely resembles the networks on the STRING web site. *stringApp* also allows users to change the confidence score and to expand the resulting network by adding an arbitrary number of nodes this can be either proteins from the same organism, proteins involved in virus-host interactions, or chemical compounds. STITCH: protein/compound query - enter a list of protein or compound names to obtain a network for them from STITCHįor each query, the user can choose to retrieve a *full STRING network* of functional associations or a *physical subnetwork*. STRING: disease query - enter a disease name to retrieve a STRING network of the top N proteins associated with the specified disease STRING: PubMed query - enter a PubMed query and utilize text mining to get a STRING network for the top N proteins associated with the query gene symbols or UniProt identifiers/accession numbers) to obtain a STRING network for the proteins The app will be automatically installed and ready to use. Scroll down to ExpressionCorrelation and select it, then click install. Click on Apps Manager and a new window will open, showing you all the available Apps. STRING: protein query - enter a list of protein names (e.g. In cytoscape, select Apps in the menu at top of the page. Currently, four different queries are supported: Users provide a list of one or more gene, protein, compound, disease, or PubMed queries, the species, the network type, and a confidence score and *stringApp* queries the database to return the matching network. and from PubMed text mining into Cytoscape. *stringApp* imports functional associations or physical interactions between protein-protein and protein-chemical pairs from
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