The STRING database in 2021:customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets
| Autor: | Christian von Mering, David Lyon, Rebecca Kirsch, Katerina C. Nastou, Peer Bork, Marc Legeay, Tao Fang, Sampo Pyysalo, Annika L. Gable, Nadezhda Tsankova Doncheva, Damian Szklarczyk, Lars Juhl Jensen |
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| Přispěvatelé: | University of Zurich, von Mering, Christian |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
PREDICTION media_common.quotation_subject BIOLOGY Context (language use) Scientific literature Biology Adaptability DISEASE UFSP13-7 Evolution in Action: From Genomes to Ecosystems Upload Resource (project management) 1311 Genetics Genetics Database Issue media_common Information retrieval Query string IDENTIFICATION String (computer science) 10124 Institute of Molecular Life Sciences Cardiovascular and Metabolic Diseases DISCOVERY 570 Life sciences biology User interface INTEGRATION |
| Zdroj: | 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, vol. 49, no. D1, pp. D605-D612 . https://doi.org/10.1093/nar/gkaa1074 Nucleic Acids Research |
| DOI: | 10.1093/nar/gkaa1074 |
| Popis: | 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/. |
| Databáze: | OpenAIRE |
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