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The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

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Item Type:Article
Title:The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets
Creators Name:Szklarczyk, D. and Gable, A.L. and Nastou, K.C. and Lyon, D. and Kirsch, R. and Pyysalo, S. and Doncheva, N.T. and Legeay, M. and Fang, T. and Bork, P. and Jensen, L.J. and von Mering, C.
Abstract:Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein-protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING database aims to integrate all known and predicted associations between proteins, including both physical interactions as well as functional associations. To achieve this, STRING collects and scores evidence from a number of sources: (i) automated text mining of the scientific literature, (ii) databases of interaction experiments and annotated complexes/pathways, (iii) computational interaction predictions from co-expression and from conserved genomic context and (iv) systematic transfers of interaction evidence from one organism to another. STRING aims for wide coverage; the upcoming version 11.5 of the resource will contain more than 14 000 organisms. In this update paper, we describe 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. In addition, we describe how to query STRING with genome-wide, experimental data, including the automated detection of enriched functionalities and potential biases in the user's query data. The STRING resource is available online, at https://string-db.org/.
Keywords:Protein Databases, Protein Interaction Mapping, Proteins, User-Computer Interface
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press
Volume:49
Number:D
Page Range:D605-D612
Date:8 January 2021
Additional Information:"Erratum in: Nucleic Acids Res 49: D605–D612" - When this paper first published, it only had one corresponding author, Christian von Mering. It should have had three corresponding authors: Christian von Mering, Peer Bork, and Lars J. Jensen. This has now been corrected online.
Official Publication:https://doi.org/10.1093/nar/gkaa1074
PubMed:View item in PubMed

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