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Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Author information

1
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
2
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
3
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
4
Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany Max Planck Institute of Molecular Cell Biology and Genetics, 01062 Dresden, Germany.
5
European Molecular Biology Laboratory, 69117 Heidelberg, Germany bork@embl.de.
6
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark lars.juhl.jensen@cpr.ku.dk.
7
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland mering@imls.uzh.ch.

Abstract

The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.

PMID:
25352553
PMCID:
PMC4383874
DOI:
10.1093/nar/gku1003
[Indexed for MEDLINE]
Free PMC Article

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