Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis

doi:10.1186/s12870-018-1589-6

CORC > 武汉植物园 > 中国科学院武汉植物园

	Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis
	Zhang, Xiujun 3; Chen, Luonan 1; Jiang, Zhonglin 1; Zhang, Aidi 3; Liu, Xiaoping 1; Zhang, Fuping 2,3
刊名	BMC PLANT BIOLOGY
	2019-01-07
卷号	19 页码:18
关键词	Time-course gene expression data Gene regulatory network (GRN) Dynamical network biomarker (DNB) Phase transition Flower development
ISSN号	1471-2229
DOI	10.1186/s12870-018-1589-6
英文摘要	BackgroundThe flowering transition which is controlled by a complex and intricate gene regulatory network plays an important role in the reproduction for offspring of plants. It is a challenge to identify the critical transition state as well as the genes that control the transition of flower development. With the emergence of massively parallel sequencing, a great number of time-course transcriptome data greatly facilitate the exploration of the developmental phase transition in plants. Although some network-based bioinformatics analyses attempted to identify the genes that control the phase transition, they generally overlooked the dynamics of regulation and resulted in unreliable results. In addition, the results of these methods cannot be self-explained.ResultsIn this work, to reveal a critical transition state and identify the transition-specific genes of flower development, we implemented a genome-wide dynamic network analysis on temporal gene expression data in Arabidopsis by dynamic network biomarker (DNB) method. In the analysis, DNB model which can exploit collective fluctuations and correlations of different metabolites at a network level was used to detect the imminent critical transition state or the tipping point. The genes that control the phase transition can be identified by the difference of weighted correlations between the genes interested and the other genes in the global network. To construct the gene regulatory network controlling the flowering transition, we applied NARROMI algorithm which can reduce the noisy, redundant and indirect regulations on the expression data of the transition-specific genes. In the results, the critical transition state detected during the formation of flowers corresponded to the development of flowering on the 7th to 9th day in Arabidopsis. Among of 233 genes identified to be highly fluctuated at the transition state, a high percentage of genes with maximum expression in pollen was detected, and 24 genes were validated to participate in stress reaction process, as well as other floral-related pathways. Composed of three major subnetworks, a gene regulatory network with 150 nodes and 225 edges was found to be highly correlated with flowering transition. The gene ontology (GO) annotation of pathway enrichment analysis revealed that the identified genes are enriched in the catalytic activity, metabolic process and cellular process.ConclusionsThis study provides a novel insight to identify the real causality of the phase transition with genome-wide dynamic network analysis.
资助项目	National Natural Sciences Foundation of China(NSFC)[61402457] ; CAS Pioneer Hundred Talents Program ; National Project of Cause Control Theory[1716315XJ00200303]
WOS研究方向	Plant Sciences
语种	英语
出版者	BMC
WOS记录号	WOS:000455102600004
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/6217]
专题	中国科学院武汉植物园
通讯作者	Zhang, Xiujun; Chen, Luonan
作者单位	1.Chinese Acad Sci, Shanghai Inst Biol Sci, Innovat Ctr Cell Signaling Network, Key Lab Syst Biol,Inst Biochem & Cell Biol, Shanghai 200031, Peoples R China 2.Univ Chinese Acad Sci, Beijing 10049, Peoples R China 3.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Plant Germplasm Enhancement & Specially A, Wuhan 430074, Hubei, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Xiujun,Chen, Luonan,Jiang, Zhonglin,et al. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis[J]. BMC PLANT BIOLOGY,2019,19:18.
APA	Zhang, Xiujun,Chen, Luonan,Jiang, Zhonglin,Zhang, Aidi,Liu, Xiaoping,&Zhang, Fuping.(2019).Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis.BMC PLANT BIOLOGY,19,18.
MLA	Zhang, Xiujun,et al."Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis".BMC PLANT BIOLOGY 19(2019):18.