High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation data. Second, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-scale transcriptome analysis to explore the global landscape of gene expression in the curated data. We found that only a small fraction of genes were differentially expressed under multiple conditions, which might be explained by their tendency of having more network connections and shorter network distances in gene networks. Collectively, we hope that PlaD can serve as an important and comprehensive knowledgebase to the community of plant sciences, providing insightful clues to better understand the molecular mechanisms underlying plant immune responses. PlaD is freely available at http://systbio.cau.edu.cn/plad/index.php or http://zzdlab.com/plad/index.php.
高通量转录组技术已被广泛应用于植物免疫转录重编程的研究，一些公共数据库中已积累了大量的转录组数据。然而，这些数据由于缺乏标准化的注释，蕴藏在其中的巨大价值还未有效利用。本研究中，我们从模式植物拟南芥以及三个重要作物（玉米，水稻和小麦）中精选了2444个病原菌相关的基因表达样本。通过对这些数据的整理和分析，我们构建了一个用户友好的转录组数据库PlaD目前， PlaD具有以下三个重要特征。第一，它提供了大规模的植物防御反应相关的数据，主要包括基因表达数据和功能注释信息。第二，它实现了条件特异的表达谱的可视化。第三，它允许用户搜索被多种条件共同调控的基因。同时，利用储存在PlaD里的数据，我们开展了大规模的转录组学分析，旨在探索植物基因表达变化的全局特征。我们发现只有少部分基因在多个条件下发生了差异表达，这部分基因在基因功能网络中倾向于有更多的网络连接和更短的网络距离。综上，我们希望PlaD可以作为一个综合的知识库，为植物科学家们进一步研究植物免疫应答机制提供有用的线索。目前，PlaD的网址为：http://systbio.cau.edu.cn/plad/index.php 或 http://zzdlab.com/plad/index.php。





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