*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 expand the resulting network by adding an arbitrary number of nodes (protein or chemical compounds), change the confidence score, and expand the network by adding new nodes. 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 v1.1* 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.
New in *stringApp v1.3*: several different types of charts to show 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.