iNID： An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis

作     者：Daeseok Choi Jaemyung Choi Byeongsoo Kang Seungchul Lee Young-hyun Cho Ildoo Hwang Daehee Hwang 

作者机构：School of Interdisciplinary Bioscience and Bioengineering POSTECH 790-784 Pohang Republic of Korea Department of Life Sciences POSTECH 790-784 Pohang Republic of Korea Department of New Biology DGIST Daegu 711-873 Republic of Korea Division of Integrative Biosciences and Biotechnologies POSTECH 790-784 Pohang Republic of Korea Center for Systems Biology of Plant Senescence and-Life History Institute for BasicScience DGIST Daegu 711-873 Republic of Korea 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2014年第7卷第5期

页      面：792-813页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 081104[工学-模式识别与智能系统] 071009[理学-细胞生物学] 0901[农学-作物学] 0902[农学-园艺学] 0811[工学-控制科学与工程] 

基　　金：supported by grants from the Next-Generation BioGreen21 Program Institute for Basic Science Proteogenomics program, POSCO Research Fund the ABC of Global Frontier projects Mid-career Researcher Program 

主　　题：transcriptome analysis network analysis signal interplays development Arabidopsis. 

摘      要：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.