Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families

doi:10.1109/TCBB.2018.2821145

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	Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families
	Wang, Pei 1,2; Wang, Daojie 3; Lu, Jinhu4,5,6,7
	2019-05-01
发表期刊	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN	1545-5963
卷号	16 期号:3 页码:912-924
摘要	Based on structural controllability of complex networks and a constructed gene network with 9,241 nodes for Arabidopsis thaliana, we classified nodes into five categories via their roles in control or node deletion, including indispensable, neutral, dispensable, driver, and critical driver nodes. The indispensable nodes can increase the number of drivers after deletion, which are never drivers or critical drivers. About 10 percent of nodes are indispensable. However, more than 60 percent of nodes are neutral ones. More than 62 percent of nodes are drivers, which indicates the gene network is very difficult to be fully controlled. Gene Ontology (GO) enrichment analysis reveals that different sets of nodes have preferred biological functions and processes.The indispensable nodes are significantly enriched as essential genes, drought responsive and abscisic acid (ABA) independent genes, transcriptional factors (TFs), core cell cycle genes, and ABA and Gibberellin (GA) related genes. The critical drivers are enriched as receptor kinase-like genes, while shorted in WRKY TFs and functional genes that are enriched in the indispensable nodes. Robustness analysis based on node and edge additions, edge rewiring indicate the obtained conclusions are robust to network perturbations. Our investigations clarify control roles of some gene families and provide potential implications for identifying functional genes in other plant species, such as drought responsive genes and TFs.
关键词	Structural controllability Arabidopsis thaliana gene network functional gene enrichment analysis
DOI	10.1109/TCBB.2018.2821145
语种	英语
资助项目	National Key Research and Development Program of China[2016YFB0800401] ; National Natural Science Foundation of China[61773153] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[61532020] ; National Natural Science Foundation of China[11472290] ; Key Scientific Research Projects in Colleges and Universities of Henan[17A120002] ; Basal Research Fund of Henan University[yqpy20140049]
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS类目	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000471070600022
出版者	IEEE COMPUTER SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/35030
专题	系统科学研究所
通讯作者	Wang, Pei
作者单位	1.Henan Univ, Sch Math & Stat, Kaifeng 475004, Peoples R China 2.Henan Univ, Inst Appl Math, Lab Data Anal Technol, Kaifeng 475004, Peoples R China 3.Henan Univ, Coll Life Sci, State Key Lab Cotton Biol, Henan Key Lab Plant Stress Biol, Kaifeng 475004, Henan, Peoples R China 4.Beihang Univ, Sch Automat Sci & Elect Engn, State Key Lab Software Dev Environm, Beijing 100083, Peoples R China 5.Beihang Univ, Beijing Adv Innovat Ctr Big Data & Brain Machine, Beijing 100083, Peoples R China 6.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 7.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Wang, Pei,Wang, Daojie,Lu, Jinhu. Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2019,16(3):912-924.
APA	Wang, Pei,Wang, Daojie,&Lu, Jinhu.(2019).Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,16(3),912-924.
MLA	Wang, Pei,et al."Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 16.3(2019):912-924.