STRING: a database of predicted functional associations between proteins

Christian von Mering

Martijn Huynen

Daniel Jaeggi

Steffen Schmidt

Peer Bork

Berend Snel

^{European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany}^{Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany}^{Nijmegen Centre for Molecular Life Sciences p/a Centre of Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands}

^{To whom correspondence should be addressed. Email:}ed.grebledieh-lbme@krob

Received 2002 Aug 14; Accepted 2002 Sep 11.

Abstract

Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar species coverage, are often located in close proximity on the genome (in prokaryotes), and tend to be involved in gene-fusion events. The database STRING is a precomputed global resource for the exploration and analysis of these associations. Since the three types of evidence differ conceptually, and the number of predicted interactions is very large, it is essential to be able to assess and compare the significance of individual predictions. Thus, STRING contains a unique scoring-framework based on benchmarks of the different types of associations against a common reference set, integrated in a single confidence score per prediction. The graphical representation of the network of inferred, weighted protein interactions provides a high-level view of functional linkage, facilitating the analysis of modularity in biological processes. STRING is updated continuously, and currently contains 261 033 orthologs in 89 fully sequenced genomes. The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/.

Abstract

ACKNOWLEDGEMENTS

This work was supported in part by grants from the Netherlands Organization for Scientific Research (NWO), from the Deutsche Forschungsgemeinschaft, and from the Bundesministerium für Forschung und Bildung, Germany, through its contribution to the Helmholtz Network for Bioinformatics.

ACKNOWLEDGEMENTS

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