Biological interaction networks are conserved at the module level.
Biological interaction networks are conserved at the module level.
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DOI：
10.1186/1752-0509-5-134
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发表时间：
2011-08-23
影响因子：
--
通讯作者：
Bar-Joseph Z
中科院分区：
文献类型：
--
作者：
Zinman GE;Zhong S;Bar-Joseph Z
直系同源基因在密切相关的物种之间高度保守，并且生物系统通常在不同的生物体中利用相同的基因。然而，虽然序列相似性往往意味着功能相似性，相互作用的数据并没有很好地保存，即使是具有高序列相似性的蛋白质。最近的几项研究比较了高通量数据，包括表达，蛋白质-蛋白质，蛋白质-DNA和近缘物种之间的遗传相互作用，显示出比预期低得多的保守率。在这项工作中，我们收集了四种模式生物（S。酿酒酵母，S. pombe，C. elegans和D. melanogaster），并进行了系统分析，以解释当与序列数据的保守性相比时，相互作用数据的明显较低的保守性。我们首先表明，以前提出的几个假设只提供了一个有限的解释，这种较低的保护率。我们将所有的相互作用证据组合成一个集成网络，为每个物种，并确定这些集成网络的功能模块。然后，我们证明，相互作用的功能模块的一部分是保守的，在更高的速率比以前的文献中的报告，而不同的功能模块之间的相互作用，以较低的速率保守。我们表明，物种之间的保护，但主要是在模块水平。我们的研究结果表明，模块内的相互作用比不同模块中蛋白质之间的相互作用更可能是保守的。这为观察到的保守率提供了一个基于网络的解释，这也有助于解释为什么尽管参与这些过程的蛋白质相互作用的保守水平较低，但如此多的生物过程是保守的。配套网站：http://www.sb.cs.cmu.edu/CrossSP
Orthologous genes are highly conserved between closely related species and biological systems often utilize the same genes across different organisms. However, while sequence similarity often implies functional similarity, interaction data is not well conserved even for proteins with high sequence similarity. Several recent studies comparing high throughput data including expression, protein-protein, protein-DNA, and genetic interactions between close species show conservation at a much lower rate than expected. In this work we collected comprehensive high-throughput interaction datasets for four model organisms (S. cerevisiae, S. pombe, C. elegans, and D. melanogaster) and carried out systematic analyses in order to explain the apparent lower conservation of interaction data when compared to the conservation of sequence data. We first showed that several previously proposed hypotheses only provide a limited explanation for such lower conservation rates. We combined all interaction evidences into an integrated network for each species and identified functional modules from these integrated networks. We then demonstrate that interactions that are part of functional modules are conserved at much higher rates than previous reports in the literature, while interactions that connect between distinct functional modules are conserved at lower rates. We show that conservation is maintained between species, but mainly at the module level. Our results indicate that interactions within modules are much more likely to be conserved than interactions between proteins in different modules. This provides a network based explanation to the observed conservation rates that can also help explain why so many biological processes are well conserved despite the lower levels of conservation for the interactions of proteins participating in these processes. Accompanying website: http://www.sb.cs.cmu.edu/CrossSP
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影响因子：
12.3
作者：
Kuo D;Tan K;Zinman G;Ravasi T;Bar-Joseph Z;Ideker T
通讯作者：
Ideker T
DOI：
10.1126/science.1162609
发表时间：
2008-10-17
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Roguev A;Bandyopadhyay S;Zofall M;Zhang K;Fischer T;Collins SR;Qu H;Shales M;Park HO;Hayles J;Hoe KL;Kim DU;Ideker T;Grewal SI;Weissman JS;Krogan NJ
通讯作者：
Krogan NJ
影响因子：
4.3
作者：
Langfelder P;Luo R;Oldham MC;Horvath S
通讯作者：
Horvath S
影响因子：
30.8
作者：
Rustici, G;Mata, J;Bähler, J
通讯作者：
Bähler, J
影响因子：
64.8
作者：
Gavin, AC;Aloy, P;Superti-Furga, G
通讯作者：
Superti-Furga, G