Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden.
Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden.
J Mol Biol. 2021 May 28;433(11):166835. doi: 10.1016/j.jmb.2021.166835. Epub 2021 Feb 2.
FunCoup (https://funcoup.sbc.su.se) is one of the most comprehensive functional association networks of genes/proteins available. Functional associations are inferred by integrating different types of evidence using a redundancy-weighted naïve Bayesian approach, combined with orthology transfer. FunCoup's high coverage comes from using eleven different types of evidence, and extensive transfer of information between species. Since the latest update of the database, the availability of source data has improved drastically, and user expectations on a tool for functional associations have grown. To meet these requirements, we have made a new release of FunCoup with updated source data and improved functionality. FunCoup 5 now includes 22 species from all domains of life, and the source data for evidences, gold standards, and genomes have been updated to the latest available versions. In this new release, directed regulatory links inferred from transcription factor binding can be visualized in the network viewer for the human interactome. Another new feature is the possibility to filter by genes expressed in a certain tissue in the network viewer. FunCoup 5 further includes the SARS-CoV-2 proteome, allowing users to visualize and analyze interactions between SARS-CoV-2 and human proteins in order to better understand COVID-19. This new release of FunCoup constitutes a major advance for the users, with updated sources, new species and improved functionality for analysis of the networks.
Funcoup（https://funcoup.sbc.su.se）是目前最全面的基因/蛋白质功能关联网络之一。功能关联是通过使用冗余加权朴素贝叶斯方法整合不同类型的证据，并结合同源物转移来推断的。Funcoup 的高覆盖率来自于使用十一种不同类型的证据，以及在物种之间广泛的信息传递。自数据库的最新更新以来，源数据的可用性有了显著改善，用户对功能关联工具的期望也有所增加。为了满足这些要求，我们发布了新版本的 Funcoup，更新了源数据并改进了功能。Funcoup 5 现在包括来自所有生命领域的 22 个物种，证据、黄金标准和基因组的源数据已更新至最新版本。在这个新版本中，可以在人类相互作用网络的网络查看器中可视化从转录因子结合推断出的有向调控链接。另一个新功能是可以在网络查看器中按特定组织中表达的基因进行过滤。Funcoup 5 还包括 SARS-CoV-2 蛋白质组，允许用户可视化和分析 SARS-CoV-2 与人类蛋白质之间的相互作用，以便更好地了解 COVID-19。Funcoup 的这个新版本为用户提供了重大进展，更新了来源、新的物种，并改进了网络分析的功能。
