Saccharomyces cerevisiae, budding yeast, is a widely used model organism and research tool in genetics studies. Many efforts have been directed at constructing a high‐quality comprehensive molecular interaction network to elucidate the design logic of the gene circuitries in this classic model organism. In this work, we present the yeast interactome resource (YIR), which includes 22,238 putative functional gene interactions inferred from functional gene association data integrated from 10 databases focusing on diverse functional perspectives. These putative functional gene interactions are expected to cover 18.84% of yeast protein interactions, and 38.49% may represent protein interactions. Based on the YIR, a gene set linkage analysis (GSLA) web tool was developed to annotate the potential functional impacts of a set of transcriptionally changed genes. In a case study, we show that the YIR/GSLA system produced more extensive and concise annotations compared with widely used gene set annotation tools, including PANTHER and DAVID. Both YIR and GSLA are accessible through the website http://yeast.biomedtzc.cn.

中文翻译：

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预测的酵母相互作用组和基于网络的转录改变基因解释。

酿酒酵母芽殖酵母是遗传学研究中广泛使用的模式生物和研究工具。许多努力致力于构建高质量的综合分子相互作用网络，以阐明这种经典模式生物中基因电路的设计逻辑。在这项工作中，我们展示了酵母相互作用组资源 (YIR)，其中包括 22,238 个假定的功能基因相互作用，这些相互作用是从功能基因关联数据中推断出来的，这些数据整合自 10 个数据库，重点关注不同的功能观点。这些假定的功能基因相互作用预计将覆盖酵母蛋白质相互作用的 18.84%，而 38.49% 可能代表蛋白质相互作用。基于 YIR，开发了基因集连锁分析 (GSLA) 网络工具来注释一组转录改变基因的潜在功能影响。在一个案例研究中，我们表明，与广泛使用的基因集注释工具（包括 PANTHER 和 DAVID）相比，YIR/GSLA 系统产生了更广泛和更简洁的注释。YIR 和 GSLA 均可通过网站 http://yeast.biomedtzc.cn 访问。