*stringApp* imports protein-protein and protein-chemical interaction data from
[http://diseases.jensenlab.org/ 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, and a confidence score and *stringApp* will query the database and return the matching network. Currently, four different queries are supported:
- STRING: protein query -- enter a list of protein names (e.g. gene symbols or UniProt identifiers/accession numbers) to obtain a STRING network for the proteins
- 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
- STRING: disease query -- enter a disease name to retrieve a STRING network of the top N proteins associated with the specified disease
- STITCH: protein/compound query -- enter a list of protein or compound names to obtain a network for them from STITCH
*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. 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 Pathways, and protein domains at a user-specified significance threshold and show the results in a new table in the Table Panel. The app provides several different types of charts to show the enriched terms. Note that you need to install the [http://apps.cytoscape.org/apps/enhancedgraphics enhancedGraphics] app for the charts to show.
*stringApp* supports automation from both commands and CyREST.