Competition-cooperation relationship networks characterize the competition and cooperation between proteins.
Competition-cooperation relationship networks characterize the competition and cooperation between proteins.
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竞争-合作关系网络表征蛋白质之间的竞争与合作
DOI：
10.1038/srep11619
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发表时间：
2015-06-25
影响因子：
4.6
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Li H;Zhou Y;Zhang Z
通过分析蛋白质-蛋白质相互作用（PPI）网络，人们可以发现一种蛋白质可能有多个结合伙伴。然而，仅从二元 PPI 很难确定与这些伙伴的相互作用是否同时发生。在这里，我们基于蛋白质结构相互作用组构建了酵母和人类竞争合作关系网络（CCRN），以清楚地展示同一蛋白质的两个伙伴之间的关系（竞争或合作）。如果两个合作伙伴竞争同一个交互界面，他们就会通过竞争优势联系在一起；否则，它们将通过合作优势连接起来。 CCRN 分析了三种中心（即竞争中心、适度中心和合作中心）的属性。我们的结果表明，竞争性中心在人类 CCRN 中具有较高的聚类系数并形成簇，但在酵母 CCRN 中没有观察到这些趋势。我们发现人类特异性蛋白质对这些差异有显着贡献。随后，我们进行了一系列计算实验来研究避免蛋白质之间竞争的调节机制。我们的综合分析表明，对于大多数酵母和人类蛋白质竞争者来说，转录调控起着重要作用。此外，人类特异性蛋白质特别偏好其他调节机制，例如选择性剪接。
By analyzing protein-protein interaction (PPI) networks, one can find that a protein may have multiple binding partners. However, it is difficult to determine whether the interactions with these partners occur simultaneously from binary PPIs alone. Here, we construct the yeast and human competition-cooperation relationship networks (CCRNs) based on protein structural interactomes to clearly exhibit the relationship (competition or cooperation) between two partners of the same protein. If two partners compete for the same interaction interface, they would be connected by a competitive edge; otherwise, they would be connected by a cooperative edge. The properties of three kinds of hubs (i.e., competitive, modest, and cooperative hubs) are analyzed in the CCRNs. Our results show that competitive hubs have higher clustering coefficients and form clusters in the human CCRN, but these tendencies are not observed in the yeast CCRN. We find that the human-specific proteins contribute significantly to these differences. Subsequently, we conduct a series of computational experiments to investigate the regulatory mechanisms that avoid competition between proteins. Our comprehensive analyses reveal that for most yeast and human protein competitors, transcriptional regulation plays an important role. Moreover, the human-specific proteins have a particular preference for other regulatory mechanisms, such as alternative splicing.
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DEG 10，必需基因数据库的更新，包括蛋白质编码基因和非编码基因组元件
影响因子：
14.9
作者：
Luo H;Lin Y;Gao F;Zhang CT;Zhang R
通讯作者：
Zhang R
影响因子：
12.3
作者：
Ekman D;Light S;Björklund AK;Elofsson A
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影响因子：
56.9
作者：
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DOI：
10.1073/pnas.1200678109
发表时间：
2012-06-12
影响因子：
11.1
作者：
Kundrotas, Petras J.;Zhu, Zhengwei;Vakser, Ilya A.
通讯作者：
Vakser, Ilya A.
影响因子：
6.4
作者：
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通讯作者：
Kolligs, Frank T.