iNID: An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis
iNID: An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis
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DOI：
10.1093/mp/sst173
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发表时间：
2014-05-01
期刊：
影响因子：
27.5
通讯作者：
Hwang, Daehee
中科院分区：
文献类型：
--
作者：
Choi, Daeseok;Choi, Jaemyung;Hwang, Daehee
植物的生长发育离不开内外信号的整合，这涉及由内外因子(IEF)激活的信号通路之间复杂的相互作用。然而，破译这些复杂的相互作用仍然具有挑战性。在这里，我们提出了一个基于网络的平台，它识别了拟南芥发育信号(INID)之间的关键调控因子和网络模型之间的相互作用。INID提供了一个全面的资源，包括(1)以前在IEF处理条件下收集的转录本，以及(2)拟南芥中的蛋白质和遗传互作组数据。此外，INID还提供了一系列工具，用于使用转录组和互动组数据识别与IEF之间相互作用相关的关键调节器和网络模型。为了证明INID的有效性，我们研究了(1)植物激素和光以及(2)植物激素和生物胁迫之间的相互作用。结果揭示了34个相互作用的潜在调控因子，其中一些尚未与相互作用相关的报道，还揭示了34个调节因子参与相互作用的网络模型，为理解由植物激素、光和生物胁迫共同定义的相互作用提供了新的见解。然后，我们通过实验验证了BME3和TEM1参与了生长素-油菜素类固醇(BR)-蓝光的相互作用。因此，INID是一个有用的工具，可以为理解IEF之间的相互作用提供基础。
Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.