stringApp

Import and augment Cytoscape networks from STRING
*stringApp* imports protein-protein and protein-chemical interaction data from STRING [https://string-db.org/] and STITCH http://stitch.embl.de/ into Cytoscape. Users provide a list of one or more gene, protein or compound identifiers, 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. 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. All STRING networks are visualized using a new "String Style" custom graphic, which closely resembles the networks on the STRING web site.

1.1.1

Works with Cytoscape 3.3

Release Notes

Minor release that handles changes to Stitch API.

1.1.0

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

**stringApp v1.1** provides two major new features: - The ability to query STITCH for networks that include both proteins and their interacting compounds. - The ability to retrieve functional enrichment information 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. **stringApp v1.1** also takes advantage of *chemViz2* and *enhancedGraphics*, if loaded, to display the 2D structures of compounds and nicer labels, respectively.

1.0.5

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

This version adds command line/REST support and changes the network naming convention to include information about the query in the network name. We also handle duplicate network names more gracefully.

1.0.4

Works with Cytoscape 3.3

Release Notes

Minor release that handles upcoming changes to String API.

1.0.3

Works with Cytoscape 3.3

Release Notes

Another update to support re-establishment of the "string-ness" of a network after merging two networks by setting the confidence value. Also fixes bug that prevented from side panel from working when a session was reloaded.

1.0.2

Works with Cytoscape 3.3

Release Notes

Fix minor issues where GeneCards links were shown for species other than Homo sapiens (GeneCards only has human genes)

1.0.1

Works with Cytoscape 3.3

Release Notes

This release fixes a simple bug to the term resolution panel that required users to unselect and reselect at least one term before the "Import" button was enabled.

1.0.0

Works with Cytoscape 3.3

Release Notes

stringApp now supports two new query styles: query for disease associated networks and query for text associated networks (based on a pubmed query). Each of these is provided as a separate "Data Source" in the Import Networks from Public Databases" dialog. This version also includes a new side panel (Apps->STRING->Show results panel) and provides links to cellular compartments, tissues, and disease information for those nodes that have that information.

0.9.2

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

This release provides some slight improvements to the rendering of the nodes, including clipping the protein images. Also added a slider to the import panel that allows users to select the number of additional nodes that get imported.

0.9.1

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

This version fixes a bug that incorrectly enabled the Import button during term resolution. Now, the import button is only enabled after all terms have at least one selected id.

0.9

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 1.1.1

Released 18 Sep 2017

Works with Cytoscape 3.3

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