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README.md

GIT repository of the stringApp for Cytoscape

stringApp imports protein-protein and protein-chemical interaction data 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, 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 "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 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 enhancedGraphics app for the charts to show.

Since version 1.6, stringApp is also integrated with the clusterMaker and EnrichmentMap apps. With the former, users can quickly cluster a STRING network using MCL clustering, while with the latter it is possible to create an enrichment map from the STRING erncihemtn results.

stringApp supports automation from both commands and CyREST.

See also:

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Cytoscape interface to STRING and STITCH

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