Co-expression among constituents of a motif in the protein-protein interaction network.
Co-expression among constituents of a motif in the protein-protein interaction network.
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DOI：
10.1142/s0219720009003959
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发表时间：
2009-02
影响因子：
1
通讯作者：
Lu H
中科院分区：
文献类型：
--
作者：
Bhardwaj N;Lu H
几乎所有的细胞功能都是各种蛋白质之间良好协调相互作用的结果。相互作用网络中连接更紧密的枢纽或基序预计将更重要，并且该基序中的任何扰动都将对相关功能的平稳性能造成更大的破坏。因此，必须推导出这些枢纽的一些一致鲁棒性。在这里，我们提供了全球性的证据表明，相互作用枢纽获得其鲁棒性对不均匀的蛋白质浓度通过共表达的成分和程度的共表达强烈相关的嵌入式基序的复杂性。我们计算了嵌入在3-，4-，5-和6-节点的相互作用图案的复杂性增加的蛋白质之间的基因表达相关性，并将它们与来自类似复杂性的随机图案的蛋白质之间的相关性进行了比较。我们发现，随着这些基序的连接性增加，组成蛋白质之间的共表达更高。例如，当表达相关性为0.7时，相关性的核密度从具有3条边的4节点基序的0.152增加到4节点团的0.403。这意味着相互作用系统的鲁棒性来自于通过共表达的基序成分之间的成比例的同步性。我们进一步表明，这种生物学的一致性，通过共表达的组分蛋白质，可以通过在分析中整合保守数据得到加强。例如，在添加来自其他基因组的进化信息时，当它们的表达相关性为0.8时，在酵母中5-和6-节点集团的情况下，相互作用和随机数据的核密度的比率分别从37.8增加到123和98.4增加到1300。我们的研究结果表明，基因的产品涉及的基序有转录和翻译特性，最大限度地减少噪音在最终的蛋白质浓度，相比随机的基因组。
Almost all cellular functions are results of well-coordinated interactions between various proteins. A more connected hub or motif in the interaction network is expected to be more important and any perturbation in this motif would be more damaging to the smooth performance of the related functions. Thus, some coherent robustness of these hubs has to be derived. Here we provide the global evidence that interaction hubs obtain their robustness against uneven protein concentrations through co-expression of the constituents and the degree of co-expression correlates strongly with the complexity of the embedded motif. We calculate the gene expression correlations between the proteins embedded in 3-, 4-, 5- and 6-node interaction motifs of increasing complexities and compared them to those between proteins from random motifs of similar complexities. We find that as the connectedness of these motifs increase, there is a higher co-expression between the constituent proteins. For example, when the expression correlation is 0.7, the kernel density of the correlation increases from 0.152 for 4-node motifs with 3 edges to 0.403 for 4-node cliques. This implies that the robustness of the interaction system emerges from a proportionate synchronicity among the constituents of the motif via co-expression. We further show that such biological coherence via co-expression of component proteins can be reinforced by integrating conservation data in the analysis. For example, on addition of evolutionary information from other genomes, the ratio of kernel density for interaction and random data in the case of 5- and 6-node cliques in yeast increases from 37.8 to 123 and 98.4 to 1300, respectively, when their expression correlation is 0.8. Our results show that genes whose products are involved in motifs have transcription and translation properties that that minimize the noise in final protein concentrations, compared to random sets of genes.