stringApp imports functional associations or physical interactions between protein-protein and protein-chemical pairs from STRING, Viruses.STRING, STITCH, DISEASES and from PubMed text mining into Cytoscape. 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. Currently, five different queries are supported:
For each query, the user can choose to retrieve a full STRING network of functional associations or a physical subnetwork.
stringApp also allows users to change the confidence score, the type of interactions, 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. All STRING networks are visualized using a new "String Style" custom graphic, which closely resembles the networks on the STRING web site.
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. It is also possible to perform the enrichment analysis automatically for several groups of nodes such as resulting from clustering. For visualization of the enrichment results, the app provides different types of charts to show the enriched terms. Note that you need to install the enhancedGraphics app for the charts to show.
stringApp supports automation from both commands and CyREST.
