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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.

Author information

1
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
2
Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94158-2517, USA.
3
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
4
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
5
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany bork@embl.de.
6
Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
7
Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.
8
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
9
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark lars.juhl.jensen@cpr.ku.dk.
10
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland mering@imls.uzh.ch.

Abstract

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/.

PMID:
27924014
PMCID:
PMC5210637
DOI:
10.1093/nar/gkw937
[Indexed for MEDLINE]
Free PMC Article

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