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PMID: 25352553 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 43 ·No. Database issue ·2015-01-00 ·Pages D447-52

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

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.

MeSH Terms
Databases, Protein Gene Expression Profiling Internet Protein Interaction Mapping Proteins/classification,genetics,metabolism Software
Chemicals
Proteins
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Szklarczyk Damian
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Franceschini Andrea
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Wyder Stefan
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Forslund Kristoffer
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Heller Davide
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Huerta-Cepas Jaime
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Simonovic Milan
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Roth Alexander
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
Santos Alberto
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
Tsafou Kalliopi P
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
Kuhn Michael
Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany Max Planck Institute of Molecular Cell Biology and Genetics, 01062 Dresden, Germany.
Bork Peer
European Molecular Biology Laboratory, 69117 Heidelberg, Germany [email protected].
Jensen Lars J
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark [email protected].
von Mering Christian
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland [email protected].
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gku1003
Email
[email protected]
[email protected]
[email protected]
Published
2015-01-00
Epub
2014-00-28
Pages
D447-52
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4383874
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gku1003 PMC Full Text View journal details
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