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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

The STRING database in 2021 : customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. / Szklarczyk, Damian; Gable, Annika L.; Nastou, Katerina C.; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo; Doncheva, Nadezhda T.; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars J.; von Mering, Christian.

In: Nucleic Acids Symposium Series, Vol. 49, No. D1, 2021, p. D605-D612.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Szklarczyk, D, Gable, AL, Nastou, KC, Lyon, D, Kirsch, R, Pyysalo, S, Doncheva, NT, Legeay, M, Fang, T, Bork, P, Jensen, LJ & von Mering, C 2021, 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets', Nucleic Acids Symposium Series, vol. 49, no. D1, pp. D605-D612. https://doi.org/10.1093/nar/gkaa1074

APA

Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, L. J., & von Mering, C. (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Symposium Series, 49(D1), D605-D612. https://doi.org/10.1093/nar/gkaa1074

Vancouver

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Symposium Series. 2021;49(D1):D605-D612. https://doi.org/10.1093/nar/gkaa1074

Author

Szklarczyk, Damian ; Gable, Annika L. ; Nastou, Katerina C. ; Lyon, David ; Kirsch, Rebecca ; Pyysalo, Sampo ; Doncheva, Nadezhda T. ; Legeay, Marc ; Fang, Tao ; Bork, Peer ; Jensen, Lars J. ; von Mering, Christian. / The STRING database in 2021 : customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. In: Nucleic Acids Symposium Series. 2021 ; Vol. 49, No. D1. pp. D605-D612.

Bibtex

@article{0a4ddb109fd942b299db4406d1c6c7b7,
title = "The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets",
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.",
keywords = "PREDICTION, INTEGRATION, DISEASE, IDENTIFICATION, DISCOVERY, BIOLOGY",
author = "Damian Szklarczyk and Gable, {Annika L.} and Nastou, {Katerina C.} and David Lyon and Rebecca Kirsch and Sampo Pyysalo and Doncheva, {Nadezhda T.} and Marc Legeay and Tao Fang and Peer Bork and Jensen, {Lars J.} and {von Mering}, Christian",
year = "2021",
doi = "10.1093/nar/gkaa1074",
language = "English",
volume = "49",
pages = "D605--D612",
journal = "Nucleic acids symposium series",
issn = "0261-3166",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - The STRING database in 2021

T2 - customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

AU - Szklarczyk, Damian

AU - Gable, Annika L.

AU - Nastou, Katerina C.

AU - Lyon, David

AU - Kirsch, Rebecca

AU - Pyysalo, Sampo

AU - Doncheva, Nadezhda T.

AU - Legeay, Marc

AU - Fang, Tao

AU - Bork, Peer

AU - Jensen, Lars J.

AU - von Mering, Christian

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - PREDICTION

KW - INTEGRATION

KW - DISEASE

KW - IDENTIFICATION

KW - DISCOVERY

KW - BIOLOGY

U2 - 10.1093/nar/gkaa1074

DO - 10.1093/nar/gkaa1074

M3 - Journal article

C2 - 33237311

VL - 49

SP - D605-D612

JO - Nucleic acids symposium series

JF - Nucleic acids symposium series

SN - 0261-3166

IS - D1

ER -

ID: 256214711