Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families
文献类型：期刊论文
| 作者 | Wang, Pei2,3; Wang, Daojie4; Lu, Jinhu1,5,6,7
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| 刊名 | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
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| 出版日期 | 2019-05-01 |
| 卷号 | 16期号:3页码:912-924 |
| 关键词 | Structural controllability Arabidopsis thaliana gene network functional gene enrichment analysis |
| ISSN号 | 1545-5963 |
| DOI | 10.1109/TCBB.2018.2821145 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000471070600022 |
| 出版者 | IEEE COMPUTER SOC |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/35029]  |
| 专题 | 系统科学研究所 |
| 通讯作者 | Wang, Pei |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Henan Univ, Sch Math & Stat, Kaifeng 475004, Peoples R China 3.Henan Univ, Inst Appl Math, Lab Data Anal Technol, Kaifeng 475004, Peoples R China 4.Henan Univ, Coll Life Sci, State Key Lab Cotton Biol, Henan Key Lab Plant Stress Biol, Kaifeng 475004, Henan, Peoples R China 5.Beihang Univ, Sch Automat Sci & Elect Engn, State Key Lab Software Dev Environm, Beijing 100083, Peoples R China 6.Beihang Univ, Beijing Adv Innovat Ctr Big Data & Brain Machine, Beijing 100083, 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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