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 functional associations or physical interactions between protein-protein and protein-chemical pairs 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, the network type, and a confidence score and *stringApp* queries the database to return the matching network. Currently, five 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 - STRING: cross-species query -- choose two species to obtain a STRING network between and within the proteins of the interacting species For each query, the user can choose to retrieve a *full STRING network* of functional associations or a *physical subnetwork*. *stringApp* also allows users to change the confidence score, the type of interactions, 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, Reactome and Wiki Pathways, DISEASES, COMPARTMENTS, TISSUES, and protein domains at a user-specified significance threshold and show the results in a new table in the Table Panel. It is also possible to perform the enrichment analysis automatically for several groups of nodes such as resulting from clustering. For visualization of the enrichment results, the app provides 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.
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2.2.0

Works with Cytoscape 3.8

Release Notes

This release makes sure that stringApp will continue working beyond 31st December 2024. Due to some necessary server reorganization, stringApp now makes better use of the STRING API by getting all protein-protein interactions directly from there. Additional interactions such as protein-compound, compound-compound, and cross-species as well as additional node information including tissue and compartments scores will still be retrieved via Jensenlab API. Besides several bug fixes, a new functionality of stringApp v2.2 is the way STITCH compound networks are created and expanded. Namely, if you query for only one protein, the returned network will contain this protein and the 10 compounds interacting with it with the highest confidence. Similarly, if you query for one compound, you will get a network of this compound and the 10 highest scoring protein interactors. In order to expand a protein-compound network, you will need to choose if you will expand from the set of proteins or the set of compounds in your network, which works the same way as expanding from a selection of protein or compound nodes.

2.1.1

Works with Cytoscape 3.8

Release Notes

Fixes a bug causing an error when sending STRING networks from the web interface to Cytoscape for some species.

2.1.0

Works with Cytoscape 3.8

Release Notes

New features: - New Edge panel that shows the subscores (scores for different evidence channels) and includes a link to the STRING edge page, where the evidence can be further explored - Ability to create networks for custom species that were uploaded by the user to STRING using the "Add organism" feature - New backend for resolving compound and viral protein identifiers Bug fixes and minor improvements: - Linkout to UniProtKB is fixed. - Compounds and viral proteins now have a description - There is a linkout to the origin of the structure image (e.g. PDB or AlphaFold)

2.0.3

Works with Cytoscape 3.8

Release Notes

Fixed a bug that accidentally removed the string disease query command.

2.0.2

Works with Cytoscape 3.8

Release Notes

This release comes with a few modifications in connection with STRING v12 being released. They include a new flat node design and update of the results panel for switching between different node styles as well as dynamic fetching of 3D protein structures and an updated internal species files.

2.0.1

Works with Cytoscape 3.8

Release Notes

This is a bug fix release to improve the *string filter enrichment* command and the connectivity with the Omics Visualizer app. A new command *string list selected species* was also added.

2.0.0

Works with Cytoscape 3.8

Release Notes

Main new features in this update: - new STRING:cross-species query type for host-parasite and virus-host interactions - new species GUI input supporting all species in STRING 10.5 - group-wise enrichment functionality - add enriched term to network - improved STRINGify functionality

1.7.1

Works with Cytoscape 3.8

Release Notes

This is a bug fix release with focus on improving the enrichment panels, support for the new network type (physical interactions) and extended species list from STRING v11.5.

1.7.0

Works with Cytoscape 3.8

Release Notes

This version of the app comes with several new features: - Enabled network queries for physical interactions from STRING v11.5 - Added an option to change the network type between *full STRING network* and *physical subnetwork* - New enrichment categories available due to the STRING update: WikiPathways, DISEASES, TISSUES, COMPARTMENTS - Enrichment panel: selection of a node in the network view automatically selects the enriched terms annotating this node - Edge Results panel: added a slider and buttons to hide/delete or show/fetch edges based on confidence and to change the network type - Replaced the show/hide menus with checkbox menus - Added documentation for commands & fixed some bugs in the commands - Fixed node/edge filter initiation to be based on the attribute values

1.6.0

Works with Cytoscape 3.8

Release Notes

This version includes the following new features in addition to some bug fixes: - Improved _stringify_ functionality: support of networks with both string and non-string nodes - Integration with _EnrichmentMap_: support for creating EM networks from STRING Enrichment results - Integration with _clusterMaker_: initiate MCL clustering from within the STRING Results panel

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 2.2.0

Released 30 Dec 2024

Works with Cytoscape 3.8

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