The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

2017 | Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork, Lars J Jensen, Christian von Mering
The STRING database, updated to version 10.5 in 2017, provides a comprehensive, quality-controlled protein-protein association network for a wide range of organisms. It integrates both experimentally validated and predicted interactions, including direct physical and indirect functional associations. The database uses multiple sources for interaction predictions, such as co-expression analysis, shared selective signals, text mining of scientific literature, and computational transfer of interaction knowledge based on gene orthology. The web interface has been redesigned to reduce dependency on outdated technologies and to improve usability, while the database can now be queried within Cytoscape. Additional features include automated background analysis of user inputs for functional enrichments and streamlined download options. The STRING resource is available online at http://string-db.org/. STRING aims to stand out by offering comprehensive coverage of organisms, intuitive web interface, Cytoscape integration, and rigorous quality control with benchmarked confidence scores for each interaction. The database includes seven evidence channels, each contributing to the final confidence score of an interaction. These channels include experimental evidence, database curation, text mining, co-expression, neighborhood, fusion, and co-occurrence. Interactions are also transferred between organisms based on orthology relationships, which is particularly useful for poorly studied organisms. The STRING database is accessible through various interfaces, including a REST API, an R package, and a web-based interface. The web interface allows users to search for networks, visualize interactions, and perform enrichment analysis. The database also supports integration with Cytoscape through a dedicated app, enabling users to retrieve, visualize, and analyze networks of hundreds to thousands of proteins. The app allows users to query networks by protein names, disease, or PubMed abstracts, and provides additional information such as subcellular localization and tissue expression data. The database is continuously updated and has been used in numerous publications. Future developments include expanding coverage to over 4000 organisms and creating a specialized database for virus-host protein-protein interactions. The database also aims to enhance user input analysis for gene sets, allowing for more detailed functional enrichment analysis. Overall, STRING serves as a crucial resource for understanding protein interactions and their functional implications in various biological contexts.The STRING database, updated to version 10.5 in 2017, provides a comprehensive, quality-controlled protein-protein association network for a wide range of organisms. It integrates both experimentally validated and predicted interactions, including direct physical and indirect functional associations. The database uses multiple sources for interaction predictions, such as co-expression analysis, shared selective signals, text mining of scientific literature, and computational transfer of interaction knowledge based on gene orthology. The web interface has been redesigned to reduce dependency on outdated technologies and to improve usability, while the database can now be queried within Cytoscape. Additional features include automated background analysis of user inputs for functional enrichments and streamlined download options. The STRING resource is available online at http://string-db.org/. STRING aims to stand out by offering comprehensive coverage of organisms, intuitive web interface, Cytoscape integration, and rigorous quality control with benchmarked confidence scores for each interaction. The database includes seven evidence channels, each contributing to the final confidence score of an interaction. These channels include experimental evidence, database curation, text mining, co-expression, neighborhood, fusion, and co-occurrence. Interactions are also transferred between organisms based on orthology relationships, which is particularly useful for poorly studied organisms. The STRING database is accessible through various interfaces, including a REST API, an R package, and a web-based interface. The web interface allows users to search for networks, visualize interactions, and perform enrichment analysis. The database also supports integration with Cytoscape through a dedicated app, enabling users to retrieve, visualize, and analyze networks of hundreds to thousands of proteins. The app allows users to query networks by protein names, disease, or PubMed abstracts, and provides additional information such as subcellular localization and tissue expression data. The database is continuously updated and has been used in numerous publications. Future developments include expanding coverage to over 4000 organisms and creating a specialized database for virus-host protein-protein interactions. The database also aims to enhance user input analysis for gene sets, allowing for more detailed functional enrichment analysis. Overall, STRING serves as a crucial resource for understanding protein interactions and their functional implications in various biological contexts.
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