The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
复制标题
DOI：
10.1093/nar/gkaa1074
复制
发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
von Mering C
中科院分区：
文献类型：
--
作者：
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
细胞生命依赖于生物分子之间功能关联的复杂网络。在这些关联中，蛋白质-蛋白质相互作用由于其多功能性、特异性和适应性而特别重要。STRING数据库旨在整合蛋白质之间所有已知和预测的关联，包括物理相互作用和功能关联。为了实现这一目标，STRING从许多来源收集证据并进行评分：（i）科学文献的自动文本挖掘，（ii）相互作用实验和注释复合物/途径的数据库，（iii）来自共表达和保守基因组背景的计算相互作用预测，以及（iv）相互作用证据从一种生物体到另一种生物体的系统转移。STRING的目标是广泛覆盖;即将到来的资源11.5版本将包含超过14000种生物。在这篇更新论文中，我们描述了文本挖掘系统的变化，物理相互作用的新评分模式，以及用于定制，扩展和共享蛋白质网络的广泛用户界面功能。此外，我们描述了如何查询字符串与全基因组，实验数据，包括丰富的功能和用户的查询数据中的潜在偏见的自动检测。STRING资源可在https://string-db.org/在线获得。
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/.
登录
查看更多内容
影响因子：
14.9
作者：
Kamburov A;Stelzl U;Lehrach H;Herwig R
通讯作者：
Herwig R
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
5.8
作者：
Gligorijevic, Vladimir;Barot, Meet;Bonneau, Richard
通讯作者：
Bonneau, Richard
影响因子：
12.3
作者：
Dalgleish, Raymond;Flicek, Paul;Maglott, Donna R.
通讯作者：
Maglott, Donna R.
影响因子：
14.9
作者：
Franceschini A;Szklarczyk D;Frankild S;Kuhn M;Simonovic M;Roth A;Lin J;Minguez P;Bork P;von Mering C;Jensen LJ
通讯作者：
Jensen LJ