STRING v9.1: Protein-protein interaction networks, with increased coverage and integration

A. Franceschini; M. Simonovic; A. Roth; C. Von Mering; D. Szklarczyk; Sune Pletscher-Frankild; L.J. Jensen; Melanie Michelsen Kuhn; J. Lin; P. Minguez; P. Bork

doi:10.1093/nar/gks1094

STRING v9.1: Protein-protein interaction networks, with increased coverage and integration

A. Franceschini, M. Simonovic, A. Roth, C. Von Mering, D. Szklarczyk, Sune Pletscher-Frankild, L.J. Jensen, Melanie Michelsen Kuhn, J. Lin, P. Minguez, P. Bork

2845 Citations (Scopus)

Abstract

Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made - particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.

Original language	English
Journal	Nucleic Acids Research
Volume	41
Issue number	D1
Pages (from-to)	D808-D815
Number of pages	8
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gks1094
Publication status	Published - 1 Jan 2013

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title = "STRING v9.1: Protein-protein interaction networks, with increased coverage and integration",

abstract = "Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made - particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.",

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AU - Szklarczyk, D.

AU - Pletscher-Frankild, Sune

AU - Jensen, L.J.

AU - Kuhn, Melanie Michelsen

AU - Lin, J.

AU - Minguez, P.

AU - Bork, P.

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N2 - Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made - particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.

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STRING v9.1: Protein-protein interaction networks, with increased coverage and integration

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