Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
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具有网络基序的中心在酵母蛋白质-蛋白质相互作用网络中动态组织模块化
DOI：
10.1371/journal.pone.0001207
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发表时间：
2007-11-21
期刊：
影响因子：
3.7
通讯作者：
Chen L
中科院分区：
文献类型：
--
作者：
Jin G;Zhang S;Zhang XS;Chen L
人们已经认识到，模块化组织渗透在生物的复杂性中。在网络分析的基础上，提出了“聚会中心”和“约会中心”的概念，以理解生物分子网络模块组织的基本原理。然而，最近关于枢纽的研究表明，没有明确的证据表明“聚会枢纽”和“约会枢纽”共存。因此，一个悬而未决的问题已经提出，是否真的存在于酵母相互作用的“党枢纽”和“日期枢纽”。与以往的研究集中在枢纽的合作伙伴或枢纽周围的单个蛋白质相比，我们的工作旨在研究枢纽的网络基序或包括枢纽及其邻居在内的单个蛋白质之间的相互作用。根据枢纽的网络基序和蛋白质复合物之间的关系，我们定义了两种新类型的枢纽，“基序党枢纽”和“基序日期枢纽”，它们分别具有与原始的“党枢纽”和“日期枢纽”相同的特征。这两类枢纽的网络模体在空间分布（或细胞定位）、在微阵列数据中的共表达、控制网络拓扑结构和组织模块性方面显示出显著不同的特征。借助网络母题，我们基本上解决了以往研究中提出的“聚会中心”和“约会中心”的开放性问题。具体而言，在网络模体而不是单个蛋白质的水平上，我们发现了两种类型的枢纽，模体党枢纽（mPHs）和模体日期枢纽（mDHs），其网络模体在生物功能上显示出不同的特征。另外，本文从不同的角度对网络模体进行了研究。也就是说，我们表明，网络模体不应该仅仅被认为是一个互动模式，但被认为是一个重要的功能单元，在组织模块的网络。
It has been recognized that modular organization pervades biological complexity. Based on network analysis, ‘party hubs’ and ‘date hubs’ were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of ‘party hubs’ and ‘date hubs’. Thus, an open question has been raised as to whether or not ‘party hubs’ and ‘date hubs’ truly exist in yeast interactome. In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub's network motifs and protein complexes, we define two new types of hubs, ‘motif party hubs’ and ‘motif date hubs’, which have the same characteristics as the original ‘party hubs’ and ‘date hubs’ respectively. The network motifs of these two types of hubs display significantly different features in spatial distribution (or cellular localizations), co-expression in microarray data, controlling topological structure of network, and organizing modularity. By virtue of network motifs, we basically solved the open question about ‘party hubs’ and ‘date hubs’ which was raised by previous studies. Specifically, at the level of network motifs instead of individual proteins, we found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), whose network motifs display distinct characteristics on biological functions. In addition, in this paper we studied network motifs from a different viewpoint. That is, we show that a network motif should not be merely considered as an interaction pattern but be considered as an essential function unit in organizing modules of networks.
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