CAST-R: An application to visualize circadian and heat stress-responsive genes in plants
CAST-R: An application to visualize circadian and heat stress-responsive genes in plants
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DOI：
10.1093/plphys/kiac121
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发表时间：
2022-03-16
期刊：
影响因子：
7.4
通讯作者：
Nagel, Dawn H.
中科院分区：
文献类型：
--
作者：
Bonnot, Titouan;Gillard, Morgane B.;Nagel, Dawn H.
生物钟帮助生物体预测和协调基因对环境刺激变化的调节反应。在胁迫下，一天中的时间和生物钟都密切控制着植物反应的大小。因此，在研究环境因素的影响时，鉴定时钟调节基因是重要的。在这里，我们介绍了CAST-R，一个“闪亮”的应用程序，允许用户识别和可视化植物中的昼夜节律和热应激反应基因。更具体地说，用户可以生成和输出代表单个或多个拟南芥（Arabidopsis thaliana）基因在24小时时间过程中响应于热胁迫和在胁迫后恢复期间的转录物丰度的谱和热图。该应用程序还利用已发表的拟南芥染色质免疫沉淀测序（ChIP-Seq）数据集来可视化时钟蛋白与其目标之间的连接。此外，CAST-R提供了执行阶段（即，表达的时间）富集分析，用于来自植物内和植物外的任何物种的节律数据集。该功能结合了统计分析和图形表示，以识别基因子集内的显著过度和代表性不足的阶段。最后，转录本丰度的分布图可以从拟南芥、芜菁、大麦和水稻中产生的多个昼夜节律数据集可视化。总之，CAST-R是一个用户友好的界面，允许通过多个可视化模块快速识别昼夜节律和应激反应基因。我们预计，这个工具将使用户更容易获得时间和动态信息的相关基因，植物对环境信号的反应。
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under stresses, both time of day and the circadian clock closely control the magnitude of plant responses. The identification of clock-regulated genes is therefore important when studying the influence of environmental factors. Here, we present CAST-R, a 'Shiny' application that allows users to identify and visualize circadian and heat stress-responsive genes in plants. More specifically, users can generate and export profiles and heatmaps representing transcript abundance of a single or of multiple Arabidopsis (Arabidopsis thaliana) genes over a 24-h time course, in response to heat stress and during recovery following the stress. The application also takes advantage of published Arabidopsis chromatin immunoprecipitation-sequencing (ChIP-Seq) datasets to visualize the connections between clock proteins and their targets in an interactive network. In addition, CAST-R offers the possibility to perform phase (i.e., timing of expression) enrichment analyses for rhythmic datasets from any species, within and beyond plants. This functionality combines statistical analyses and graphical representations to identify significantly over- and underrepresented phases within a subset of genes. Lastly, profiles of transcript abundance can be visualized from multiple circadian datasets generated in Arabidopsis, Brassica rapa, barley (Hordeum vulgare), and rice (Oryza sativa). In summary, CAST-R is a user-friendly interface that allows the rapid identification of circadian and stress-responsive genes through multiple modules of visualization. We anticipate that this tool will make it easier for users to obtain temporal and dynamic information on genes of interest that links plant responses to environmental signals.