title: STRING v10: protein-protein interaction networks, integrated over the tree of life.
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.
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Franceschini
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wyder
authors.affiliation: European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Forslund
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Heller
authors.affiliation: European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Milan
authors.initials: M
authors.lastname: Simonovic
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Roth
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
authors.forename: Alberto
authors.initials: A
authors.lastname: Santos
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark.
authors.forename: Kalliopi P
authors.initials: KP
authors.lastname: Tsafou
authors.affiliation: Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany Max Planck Institute of Molecular Cell Biology and Genetics, 01062 Dresden, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kuhn
authors.affiliation: European Molecular Biology Laboratory, 69117 Heidelberg, Germany bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark lars.juhl.jensen@cpr.ku.dk.
authors.forename: Lars J
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland mering@imls.uzh.ch.
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
mesh_terms: D030562:Databases, Protein; D020869:Gene Expression Profiling; D020407:Internet; D025941:Protein Interaction Mapping; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins