stringApp

Import and augment Cytoscape networks from STRING
Categories: annotation, automation, data visualization, disease, enrichment analysis, gene-disease association, gene function prediction, import, interaction database, network generation, online data import, PPI-network, visualization
*stringApp* imports protein-protein and protein-chemical interaction data from [https://string-db.org/ STRING], [http://viruses.string-db.org/ Viruses.STRING], [http://stitch.embl.de/ STITCH], [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.
Authors:

1.5.1

Works with Cytoscape 3.7

Release Notes

This version addresses several bug fixes and minor improvements, including: * number of enriched terms are shown in enrichment tables * users can export the filtered enrichment table * stringify now also detects compound identifiers * improved handling of networks without edges * better error handling and messages to the user * new icons for the panels to use in 3.8

1.5.0

Works with Cytoscape 3.7

Release Notes

Along with some bug fixes and improvements, this version includes several new features: - New STRING panel in the Results panel with quick-access buttons and interactive node and edge filters - Custom background for enrichment retrieval (any loaded network in the session) - New results panel for enriched publications - Support for column namespaces - Improved support for user-defined proxy - Checkbox to highlight the first neighbors of a selected node

1.4.2

Works with Cytoscape 3.6

Release Notes

This version is a bug fix release and updates the list of organisms and enrichment categories in the app according to the ones in STRING v11.

1.4.1

Works with Cytoscape 3.6

Release Notes

This is mainly a bug fix release as indicated in more detail below. Note that you need this version so that the app works properly when STRING v11 goes online. - Removed limit of 2000 nodes from enrichment analysis - Added a global config file with URLs and user messages - Fixed the computation of the "score" scores - Changed layout option for new nodes after "Expand network" - Fixed several small bugs related to enrichment, user interface, and commands

1.4.0

Works with Cytoscape 3.6

Apps that depend on this release

Release Notes

Along with some bug fixes and improvements of enrichment and commands, this version includes several new features: * Support for virus-host interactions from http://viruses.string-db.org/ * Global stringApp settings * Option to enable/disable glass ball effect * Option to automatically load enrichment data * New commands for querying additional nodes and changing confidence * JSON return for all commands

1.3.2

Works with Cytoscape 3.6

Release Notes

This is a bug-fix release: * *Remove redundant terms* removes terms that have a Jaccard similarity higher than the user-specified *redundancy cutoff* with **any** of the selected terms. * Filtering of enrichment terms is preserved when switching between networks. * New option *Use Smart Delimiters* allows for delimiters other than new lines (tabs, commas, semicolons) to be automatically considered in the input query.

1.3.1

Works with Cytoscape 3.6

Release Notes

This is primarily a bug-fix release: * Resolving protein names and identifiers now works with lists bigger than 2000, thanks to in-built batch query functionality.

1.3.0

Works with Cytoscape 3.6

Release Notes

This version fixes several bugs and adds several new features to functional enrichment, including charts on the nodes showing the enriched terms, the ability to filter the enriched terms by source (GO, KEGG, etc.) and a feature that allows duplicate terms (based on Jaccard similarity) to be removed.

1.2.2

Works with Cytoscape 3.6

Apps that depend on this release

Release Notes

Fixes a bug with the diseases network search panel that resulted in the user having to interact with the resolution dialog even though no resolution was required.

1.2.1

Works with Cytoscape 3.6

Release Notes

This is primarily a bug-fix release: * When entering proteins or compounds into the network search bar, a text area is now popped up. This allows gene and compound names with spaces or commas. * Fixes to the species combo box so that the type to search feature works on Windows. * Fixes a bug where missing or incomplete species names typed into the species combo box resulted in not getting the right species. * Fixed loading of enrichment results for saved sessions.

1.2.0

Works with Cytoscape 3.6

Apps that depend on this release

Release Notes

This release of the stringApp has several new features in addition to a number of bug fixes. The new features include: * Integration with the new Cytoscape 3.6 network search interface * New species search box * Support for the export of enrichment results (see File->Export->STRING Enrichment) * Selectivity parameter in Expand by * By default, relayout the new nodes only when a network is expanded * New displayName column * New commands and existing commands support the new 3.6 REST interface * Ability to import all genes/proteins for a particular species

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 1.5.1

Released 30 Mar 2020

Works with Cytoscape 3.7

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