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

Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth; Alberto Santos Delgado; Kalliopi P Tsafou; Michael Kuhn; Peer Bork; Lars J Jensen; Christian von Mering

doi:10.1093/nar/gku1003

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

Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos Delgado, Kalliopi P Tsafou, Michael Kuhn, Peer Bork, Lars J Jensen, Christian von Mering

5246 Citations (Scopus)

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.

Original language	English
Journal	Nucleic Acids Research
Volume	43
Issue number	D1
Pages (from-to)	D447-52
Number of pages	6
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gku1003
Publication status	Published - 28 Jan 2015

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@article{27d3879988c447839d3794782c3b87e3,

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.",

author = "Damian Szklarczyk and Andrea Franceschini and Stefan Wyder and Kristoffer Forslund and Davide Heller and Jaime Huerta-Cepas and Milan Simonovic and Alexander Roth and {Santos Delgado}, Alberto and Tsafou, {Kalliopi P} and Michael Kuhn and Peer Bork and Jensen, {Lars J} and {von Mering}, Christian",

note = "{\textcopyright} The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2015",

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doi = "10.1093/nar/gku1003",

language = "English",

volume = "43",

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TY - JOUR

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T2 - protein-protein interaction networks, integrated over the tree of life

AU - Szklarczyk, Damian

AU - Franceschini, Andrea

AU - Wyder, Stefan

AU - Forslund, Kristoffer

AU - Heller, Davide

AU - Huerta-Cepas, Jaime

AU - Simonovic, Milan

AU - Roth, Alexander

AU - Santos Delgado, Alberto

AU - Tsafou, Kalliopi P

AU - Kuhn, Michael

AU - Bork, Peer

AU - Jensen, Lars J

AU - von Mering, Christian

PY - 2015/1/28

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N2 - 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.

AB - 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.

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DO - 10.1093/nar/gku1003

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C2 - 25352553

SN - 0305-1048

VL - 43

SP - D447-52

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

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

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