Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks.
Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks.
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DOI：
10.1371/journal.pcbi.1000817
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发表时间：
2010-06-17
影响因子：
4.3
通讯作者：
Jones NS
中科院分区：
文献类型：
--
作者：
Agarwal S;Deane CM;Porter MA;Jones NS
“约会”和“聚会”中心的概念在蛋白质-蛋白质相互作用网络的研究中具有影响力。约会中心与他们的合作伙伴表现出低共表达，而派对中心有高共表达。有人提议，聚会中心是地方协调员，而约会中心是全球联系人。在这里，我们表明，所报告的重要性的日期枢纽网络连接实际上可以归因于其中的一个小子集。至关重要的是，这些少数的，非常中心的，枢纽并没有显示出特别低的表达相关性，破坏了这个数量和枢纽功能之间的联系。日期/党的区别最初是出于一个近似双峰分布的枢纽共同表达，我们表明，这一功能并不总是强大的方法的变化。此外，枢纽的拓扑性质一般与共表达无关。然而，我们发现相互作用的中心性和相互作用的蛋白质的功能相似性之间的显着相关性。我们认为，在蛋白质相互作用网络的枢纽的日期/党的二分法的思想是没有意义的，它可能是更有用的设想蛋白质-蛋白质相互作用的作用，而不是单个蛋白质。蛋白质是细胞机器的关键组成部分，大多数细胞功能都是由蛋白质组协同作用执行的。对蛋白质相互作用形成的网络的研究可以帮助揭示细胞的复杂功能是如何从简单的生物化学中产生的。某些蛋白质具有特别大量的相互作用伙伴;有些人认为这些“枢纽”对生物功能至关重要。以前的研究表明，这种枢纽可以分为两种：聚会枢纽，协调特定的细胞过程或蛋白质复合物;和日期枢纽，连接在一起，并在不同的功能特定的模块或复合物之间传递信息。在本研究中，我们从多个角度重新审视了约会和聚会中心的概念。通过计算分区的蛋白质相互作用网络功能连贯的子网络，我们表明，枢纽的作用比一个二进制分类允许更多样化。我们还表明，在网络中的相互作用的位置是有关的两个相互作用的蛋白质的功能相似性：最重要的相互作用保持网络在一起似乎是最不相似的蛋白质之间。因此，研究相互作用的作用可能与理解蛋白质相互作用网络的组织有关。
The idea of “date” and “party” hubs has been influential in the study of protein–protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here, we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins. We suggest that thinking in terms of a date/party dichotomy for hubs in protein interaction networks is not meaningful, and it might be more useful to conceive of roles for protein-protein interactions rather than for individual proteins. Proteins are key components of cellular machinery, and most cellular functions are executed by groups of proteins acting in concert. The study of networks formed by protein interactions can help reveal how the complex functionality of cells emerges from simple biochemistry. Certain proteins have a particularly large number of interaction partners; some have argued that these “hubs” are essential to biological function. Previous work has suggested that such hubs can be classified into just two varieties: party hubs, which coordinate a specific cellular process or protein complex; and date hubs, which link together and convey information between different function-specific modules or complexes. In this study, we re-examine the ideas of date and party hubs from multiple perspectives. By computationally partitioning protein interaction networks into functionally coherent subnetworks, we show that the roles of hubs are more diverse than a binary classification allows. We also show that the position of an interaction in the network is related to the functional similarity of the two interacting proteins: the most important interactions holding the network together appear to be between the most dissimilar proteins. Thus, examining interaction roles may be relevant to understanding the organisation of protein interaction networks.
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影响因子：
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