Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China.
Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital Department of Radiation Oncology, Zhejiang University School of Medicine, 866 Yuhantang Rd, Hangzhou 310058, China.
Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baaa005.
Drosophila melanogaster is a well-established model organism that is widely used in genetic studies. This species enjoys the availability of a wide range of research tools, well-annotated reference databases and highly similar gene circuitry to other insects. To facilitate molecular mechanism studies in Drosophila, we present the Predicted Drosophila Interactome Resource (PDIR), a database of high-quality predicted functional gene interactions. These interactions were inferred from evidence in 10 public databases providing information for functional gene interactions from diverse perspectives. The current version of PDIR includes 102 835 putative functional associations with balanced sensitivity and specificity, which are expected to cover 22.56% of all Drosophila protein interactions. This set of functional interactions is a good reference for hypothesis formulation in molecular mechanism studies. At the same time, these interactions also serve as a high-quality reference interactome for gene set linkage analysis (GSLA), which is a web tool for the interpretation of the potential functional impacts of a set of changed genes observed in transcriptomics analyses. In a case study, we show that the PDIR/GSLA system was able to produce a more comprehensive and concise interpretation of the collective functional impact of multiple simultaneously changed genes compared with the widely used gene set annotation tools, including PANTHER and David. PDIR and its associated GSLA service can be accessed at http://drosophila.biomedtzc.cn.
黑腹果蝇是一种被广泛应用于遗传研究的成熟模式生物。该物种具有广泛的研究工具、注释良好的参考数据库以及与其他昆虫高度相似的基因调控网络。为了促进果蝇中的分子机制研究，我们构建了一个预测果蝇互作资源库（PDIR），这是一个高质量的预测功能基因互作数据库。这些互作是根据来自 10 个公共数据库的证据推断出来的，这些数据库从不同角度提供了功能基因互作的信息。目前的 PDIR 版本包含 102835 个具有平衡灵敏度和特异性的假设功能关联，预计涵盖所有果蝇蛋白互作的 22.56%。这组功能互作是分子机制研究中假设形成的良好参考。同时，这些互作也可作为基因集连锁分析（GSLA）的高质量参考互作组，这是一个用于解释转录组分析中观察到的一组变化基因的潜在功能影响的网络工具。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（如 PANTHER 和 David）相比，PDIR/GSLA 系统能够更全面、更简洁地解释多个同时变化基因的集体功能影响。PDIR 及其相关的 GSLA 服务可在 http://drosophila.biomedtzc.cn 上访问。
