Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18.
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk D1, Morris JH2, Cook H3, Kuhn M4, Wyder S1, Simonovic M1, Santos A3, Doncheva NT3, Roth A1, Bork P5,6,7,8, Jensen LJ9, von Mering C10.
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA.
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany bork@embl.de.
Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark lars.juhl.jensen@cpr.ku.dk.
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland mering@imls.uzh.ch.
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements 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/.
© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
10.1093/nar/gkw937
Network and Enrichment Analysis. Combined screenshots from the STRING website, showing results obtained upon entering a set of 31 proteins suspected to be involved in Amyotrophic Lateral Sclerosis (). The insets are showing (from top to bottom): the accessory information available for a single protein, a reported enrichment of functional connections among the set of proteins, and statistical enrichments detected in functional subsystems. In the bottom inset, one enriched function has been selected, and the corresponding protein nodes in the network are automatically highlighted in color.
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
Nucleic Acids Res. 2017 Jan 4;45(Database issue):D362-D368.
STRING network visualization within Cytoscape. Using the Cytoscape STRING app, a network was retrieved for 78 proteins interacting with TrkA (tropomyosin-related kinase A) 10 min after stimulating neuroblastoma cells with NGF (nerve growth factor) (). With a confidence cutoff of 0.4, the resulting network contains 182 functional associations between 57 of the proteins; the 21 proteins with no associations to other proteins in the network were removed. Nodes are colored according to the protein abundance (log ratio) compared to the cells before NGF treatment. The confidence score of each interaction is mapped to the edge thickness and opacity.
Computational Biology/methods*
Databases, Protein*
Protein Interaction Mapping
Protein Interaction Maps
Proteins/chemistry
Software*
P41 GM103311/GM/NIGMS NIH HHS/United States
Silverchair Information Systems