STRING 8—a global view on proteins and their functional interactions in 630 organisms

By Lars Juhl Jensen, Michael Kuhn, M. Stark, Samuel Chaffron, Christopher J. Creevey, Jean Muller, Tobias Doerks, P. Julien, Alexander C. J. Roth, Milan Simonovic and 2 more. Nucleic Acids Res., 2008

2,563 citations recorded by the source corpus.

Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein–protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures. Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein–protein interactions currently available. STRING can be reached at http://string-db.org/.

Subfields: Molecular Biology

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Citations in the corpus

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Here, we brieﬂy describe the content and procedures currently used in STRING and describe new features that have been added since our last update on the resource (40).”
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression (2016, methodology): “GNet-LMM recovered all eQTLs detected using a standard LMM and an analysis using the STRING database [47] suggested that the additional eQTL genes are embedded within functionally consistent networks (Figure S16 in Additional file 1).”
The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees (2013, methodology): “…obtained from the BioGRID [34] database), protein-protein interactions in human (Y, undirected, obtained from the BioGRID [34] and STRING [35] databases), and orthology relations between human and yeast proteins (Z, bipartite, from the InParanoid database [36]) (see right panel of Table…”
Biomedical text mining and its applications in cancer research (2013, neutral): “STRING [175,176] STRING provides known and predicted protein interactions, including physical and functional associations derived from Genomic context, high-throughput experiments, coexpression and previous knowledge Table 5 Some commonly used standard annotated data sets for text mining.”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “We have already discussed many aspects of the STRING resource previously, e.g. (31,32), including its data-sources, prediction algorithms and user-interface.”
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells (2015, methodology): “To establish whether the genes distinguishing the two clusters act in a coordinated manner, we studied their interactions using the STRING database 41 .”
Multi-view prediction of protein function (2011, neutral): “3 [13] for speciesspecific information.”
A tissue-specific atlas of mouse protein phosphorylation and expression. (2010, positive): “Mapping Protein Expression and Phosphorylation Data onto Protein Interaction Networks Protein observations with and without phosphopeptide enrichment were mapped onto the mouse STRING database of known protein interactions (Jensen et al., 2009).”
From the regulation of peptidoglycan synthesis to bacterial growth and morphology (2011, background): “-specific outer-membrane lipoprotein containing an SPR domain, PA4699 (Ref”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, background): “Inaddition, we encourage our users to explore the links to other resources that integrate information on signaling networks or protein–protein interactions, such as MINT (30) and STRING (31), to expand their knowledge of the phosphoprotein substrates.”