This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis. The latter allows us to also introduce a new class of functional association between genes - co-occurrence in the same operon. We also supplemented the existing classes of functional association: metabolic, signaling, complex and physical protein interaction with up-to-date information. In this release we switched to InParanoid v8 as the source of orthology and base for calculation of phylogenetic profiles. While populating all other evidence types with new data we introduce a new evidence type based on quantitative mass spectrometry data. Finally, the new JavaScript based network viewer provides the user an intuitive and responsive platform to further evaluate the results.

中文翻译：

---

FunCoup 4：新物种，数据和可视化

FunCoup数据库的此版本（http://funcoup.sbc.su.se）是用于全基因组功能关联网络的最全面数据库之一的第四代。这些功能关联是通过使用朴素的贝叶斯算法和基于正交学的跨不同物种的信息传递集成各种数据类型来推断的。这种方法提供了包括基因组的高覆盖率以及推断的相互作用的高质量。在FunCoup的此更新中，我们引入了四个新的真核生物种：裂殖酵母，恶性疟原虫，金牛座，水稻（Oryza sativa），并通过包含大肠杆菌和枯草芽孢杆菌的网络向原核域开放数据库。后者使我们还可以引入基因之间的新型功能关联-同一操纵子中的共现。我们还补充了现有的功能关联类别：代谢，信号传导，复杂和物理蛋白质相互作用以及最新信息。在此版本中，我们改用InParanoid v8作为矫正学的来源和系统发育谱的计算基础。在用新数据填充所有其他证据类型的同时，我们基于定量质谱数据引入了一种新的证据类型。最后，新的基于JavaScript的网络查看器为用户提供了一个直观，响应迅速的平台，可以进一步评估结果。