GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis.
GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis.
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GSHR 是一个基于网络的平台，提供拟南芥激素反应的基因集水平分析
DOI：
10.3389/fpls.2018.00023
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发表时间：
2018
影响因子：
5.6
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Ran X;Liu J;Qi M;Wang Y;Cheng J;Zhang Y
植物激素调节植物生长和环境反应的各个方面。最近的高通量技术促进了对不同激素调控基因的更全面的分析。然而，这些组学数据通常导致大量基因列表，这使得解释数据和提取生物学意义的见解具有挑战性。随着这些大规模实验的快速积累，特别是公共数据库中可获得的转录组学数据，需要一种利用这些信息来探索转录网络的方法。不同的平台具有不同的架构和设计，由于植物激素的高度动态和灵活的作用，即使是使用同一平台的类似研究也可能获得差异较大的数据；这使得在不同的研究和平台之间进行比较变得困难。在这里，我们提出了一个web服务器提供基因集水平的分析拟南芥激素反应。GSHR从基因表达总站收集了333个RNA-seq和1205个芯片数据集，表征拟南芥转录组学对植物激素的响应，包括脱落酸、生长素、油菜素类固醇、细胞分裂素、乙烯、赤霉素、栀子酸、水杨酸和独角果酸内酯。这些数据被进一步处理并组织成1368个受不同激素或激素相关因素调节的基因集。通过将输入基因列表与这些基因集进行比较，GSHR有助于从输入基因列表中识别受不同植物激素或相关因子调控的基因集。总之，GSHR将激素和相关因素诱导的转录组变化的先前信息与新生成的数据和设施联系起来，进行交叉研究和跨平台比较；这有助于从大规模数据集中挖掘具有生物学意义的信息。GSHR可在http://bioinfo.sibs.ac.cn/GSHR/免费获得。
Phytohormones regulate diverse aspects of plant growth and environmental responses. Recent high-throughput technologies have promoted a more comprehensive profiling of genes regulated by different hormones. However, these omics data generally result in large gene lists that make it challenging to interpret the data and extract insights into biological significance. With the rapid accumulation of theses large-scale experiments, especially the transcriptomic data available in public databases, a means of using this information to explore the transcriptional networks is needed. Different platforms have different architectures and designs, and even similar studies using the same platform may obtain data with large variances because of the highly dynamic and flexible effects of plant hormones; this makes it difficult to make comparisons across different studies and platforms. Here, we present a web server providing gene set-level analyses of Arabidopsis thaliana hormone responses. GSHR collected 333 RNA-seq and 1,205 microarray datasets from the Gene Expression Omnibus, characterizing transcriptomic changes in Arabidopsis in response to phytohormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonic acid, salicylic acid, and strigolactones. These data were further processed and organized into 1,368 gene sets regulated by different hormones or hormone-related factors. By comparing input gene lists to these gene sets, GSHR helped to identify gene sets from the input gene list regulated by different phytohormones or related factors. Together, GSHR links prior information regarding transcriptomic changes induced by hormones and related factors to newly generated data and facilities cross-study and cross-platform comparisons; this helps facilitate the mining of biologically significant information from large-scale datasets. The GSHR is freely available at http://bioinfo.sibs.ac.cn/GSHR/.
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