TY - JOUR
T1 - The STRING database in 2017
T2 - quality-controlled protein-protein association networks, made broadly accessible
AU - Szklarczyk, Damian
AU - Morris, John H
AU - Cook, Helen
AU - Kuhn, Michael
AU - Wyder, Stefan
AU - Simonovic, Milan
AU - Santos Delgado, Alberto
AU - Doncheva, Nadezhda T
AU - Roth, Alexander
AU - Bork, Peer
AU - Jensen, Lars J
AU - von Mering, Christian
N1 - © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2017/1
Y1 - 2017/1
N2 - 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/.
AB - 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/.
U2 - 10.1093/nar/gkw937
DO - 10.1093/nar/gkw937
M3 - Journal article
C2 - 27924014
SN - 0305-1048
VL - 45
SP - D362-D368
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -