STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Andrea Franceschini,Damian Szklarczyk,Sune Frankild,Michael Kuhn,Milan Simonovic,Alexander Roth,Jianyi Lin,Pablo Minguez,Peer Bork,Christian von Mering,Lars Juhl Jensen +10 more
TLDR
The update to version 9.1 of STRING is described, introducing several improvements, including extending the automated mining of scientific texts for interaction information, to now also include full-text articles, and providing users with statistical information on any functional enrichment observed in their networks.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.read more
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STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk,Annika L. Gable,David Lyon,Alexander Junge,Stefan Wyder,Jaime Huerta-Cepas,Milan Simonovic,Nadezhda Tsankova Doncheva,John H. Morris,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: The latest version of STRING more than doubles the number of organisms it covers, and offers an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input.
Journal ArticleDOI
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,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
TL;DR: H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Journal ArticleDOI
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk,John H. Morris,Helen Cook,Michael Kuhn,Stefan Wyder,Milan Simonovic,Alberto Santos,Nadezhda Tsankova Doncheva,Alexander Roth,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Journal ArticleDOI
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk,Annika L. Gable,Katerina C. Nastou,David Lyon,Rebecca Kirsch,Sampo Pyysalo,Nadezhda Tsankova Doncheva,Marc Legeay,Tao Fang,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: Changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks are described.
Journal ArticleDOI
SMART: recent updates, new developments and status in 2015
TL;DR: The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million and a new, vector-based display engine has been developed for protein schematics in SMART.
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TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
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