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In molecular biology, STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database and web resource of known and predicted protein–protein interactions. [1][2][3][4][5][6]

STRING home page
DescriptionSearch Tool for the Retrieval of Interacting Genes/Proteins
Research centerAcademic Consortium
Primary citationPMID 25352553
WebsiteSTRING website
Download URLurl
Web service URLrest
Version10.5 (May 2017)

The STRING database contains information from numerous sources, including experimental data, computational prediction methods and public text collections. It is freely accessible and it is regularly updated. The resource also serves to highlight functional enrichments in user-provided lists of proteins, using a number of functional classification systems such as GO, Pfam and KEGG. The latest version 10.5 contains information on about 9.6 million proteins from more than 2000 organisms. STRING has been developed by a consortium of academic institutions including CPR, EMBL, KU, SIB, TUD and UZH.



Protein–protein interaction networks are an important ingredient for the system-level understanding of cellular processes. Such networks can be used for filtering and assessing functional genomics data and for providing an intuitive platform for annotating structural, functional and evolutionary properties of proteins. Exploring the predicted interaction networks can suggest new directions for future experimental research and provide cross-species predictions for efficient interaction mapping.[7]

Protein–protein interaction network visualized by STRING. In this view, the color saturation of the edges represents the confidence score of a functional association



Data sourcesEdit

Like many other databases that store protein association knowledge, STRING imports data from experimentally derived protein–protein interactions through literature curation. Furthermore, STRING also store computationally predicted interactions from: (i) text mining of scientific texts, (ii) interactions computed from genomic features, and (iii) interactions transferred from model organisms based on orthology. [8]

All predicted or imported interactions are benchmarked against a common reference of functional partnership as annotated by KEGG (Kyoto Encyclopedia of Genes and Genomes).

Imported dataEdit

STRING imports protein association knowledge from databases of physical interaction and databases of curated biological pathway knowledge (MINT, HPRD, BIND, DIP, BioGRID, KEGG, Reactome, IntAct, EcoCyc, NCI-Nature Pathway Interaction Database, GO). Links are supplied to the originating data of the respective experimental repositories and database resources.

Text miningEdit

A large body of scientific texts (SGD, OMIM, FlyBase, PubMed) are parsed to search for statistically relevant co-occurrences of gene names.

Predicted dataEdit

  • Neighborhood: Similar genomic context in different species suggest a similar function of the proteins.
  • Fusion-fission events: Proteins that are fused in some genomes are very likely to be functionally linked (as in other genomes where the genes are not fused).
  • Coexpression: Predicted association between genes based on observed patterns of simultaneous expression of genes.


  1. ^ Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C (2015). "STRING v10: protein-protein interaction networks, integrated over the tree of life". Nucleic Acids Res. 43 (Database issue): D447–52. doi:10.1093/nar/gku1003. PMC 4383874. PMID 25352553.
  2. ^ Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ (2013). "STRING v9.1: protein-protein interaction networks, with increased coverage and integration". Nucleic Acids Res. 41 (Database issue): D808–15. doi:10.1093/nar/gks1094. PMC 3531103. PMID 23203871.
  3. ^ Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C (2011). "The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored". Nucleic Acids Res. 39 (Database issue): D561–8. doi:10.1093/nar/gkq973. PMC 3013807. PMID 21045058.
  4. ^ Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C (2009). "STRING 8—a global view on proteins and their functional interactions in 630 organisms". Nucleic Acids Res. 37 (Database issue): D412–6. doi:10.1093/nar/gkn760. PMC 2686466. PMID 18940858.
  6. ^ Snel, B; Lehmann, G; Bork, P & Huynen, MA (2000). "STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene". Nucleic Acids Res. 28 (18): 3442–4. doi:10.1093/nar/28.18.3442. PMC 110752. PMID 10982861.
  8. ^ Wodak, SJ; Pu, S; Vlasblom, J & Séraphin, B (2009). "Challenges and rewards of interaction proteomics". Mol Cell Proteomics. 8 (1): 3–18. doi:10.1074/mcp.R800014-MCP200. PMID 18799807.

External linksEdit