Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families
Controllability Analysis of a Gene Network for Arabidopsis thaliana Reveals Characteristics of Functional Gene Families
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拟南芥基因网络的可控性分析揭示功能基因家族的特征
DOI：
10.1109/tcbb.2018.2821145
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发表时间：
2019-05
期刊：
影响因子：
--
通讯作者：
Lu Jinhu
中科院分区：
文献类型：
--
作者：
Wang Pei;Wang Daojie;Lu Jinhu
基于复杂网络的结构可控性，构建了拟南芥9241个节点的基因网络，根据节点在控制或缺失节点中的作用将节点分为5类：不可或缺节点、中性节点、可缺性节点、驱动节点和关键驱动节点。不可缺少的节点在删除后会增加驱动的数量，这些节点从来不是驱动，也不是关键驱动。大约10%的节点是不可或缺的。但是，超过60%的节点是中性节点。超过62%的节点是驱动节点，这表明基因网络很难完全控制。基因本体（Gene Ontology， GO）富集分析表明，不同的节点集具有不同的生物学功能和过程。作为必需基因、干旱响应和脱落酸（ABA）独立基因、转录因子（TFs）、核心细胞周期基因以及ABA和赤霉素（GA）相关基因，不可或缺的节点显著富集。关键驱动因子富集于受体激酶样基因，而WRKY TFs和功能基因富集于不可或缺的节点。基于节点和边相加、边重布线的鲁棒性分析表明，所得结论对网络扰动具有鲁棒性。我们的研究阐明了一些基因家族的控制作用，并为其他植物物种的功能基因（如干旱响应基因和tf）的鉴定提供了潜在的启示。
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.
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影响因子：
3
作者：
Zhang XF;Ou-Yang L;Zhu Y;Wu MY;Dai DQ
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