Статья

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

Damian SzklarczykDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, SwitzerlandAnnika L GableDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, SwitzerlandKaterina NastouNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, DenmarkDavid LyonDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, SwitzerlandRebecca KirschNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, DenmarkSampo PyysaloTurkuNLP Group, Department of Future Technologies, University of Turku, 20014 Turun Yliopisto, FinlandNadezhda T. DonchevaNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, DenmarkMarc LegeayNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, DenmarkTao FangDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, SwitzerlandPeer BorkMolecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, GermanyLars Juhl JensenNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, DenmarkChristian von MeringDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland

2020en

ABI

Аннотация

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/.

Перевод пока недоступен

Идентификаторы

DOI: 10.1093/nar/gkaa1074

Цитирования и источники

Цитирований: 3Использованных источников: 0

Показатели — AkademScholar