Stable evolutionary signal in a yeast protein interaction network.
Stable evolutionary signal in a yeast protein interaction network.
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DOI：
10.1186/1471-2148-6-8
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发表时间：
2006-01-30
影响因子：
3.4
通讯作者：
Ferdig MT
中科院分区：
文献类型：
--
作者：
Wuchty S;Barabási AL;Ferdig MT
最近出现的蛋白质相互作用网络范例可以为细胞的内部工作提供新的和重要的见解。然而，假阳性和假阴性蛋白质-蛋白质相互作用数据的沉重负担让人对这些相互作用集的更广泛用途产生了怀疑。一次只关注一个蛋白质的方法已经被强有力地用来证明参与许多相互作用的蛋白质的高度保守性；在这里，我们扩展了他的“节点”关注的范式，以研究在酿酒酵母的蛋白质相互作用网络中基于“链接”的进化信号的相对持久性，并指出这一相对未被开发的信息来源的价值。高度连接的蛋白质在进化中最好是保守的趋势是稳定的，即使在潜在的蛋白质相互作用以及五种高等真核生物之间的同源性分配的巨大噪音的背景下也是如此。我们发现，相互作用周围的局部聚集与参与蛋白质的优先进化保守相关；此外，高度局部聚集与进化保守之间的相关性伴随着相互作用蛋白质的稳定的高共表达程度。我们使用这种保守的相互作用数据，结合恶性疟原虫/酵母同源基因，作为原则证明，高阶网络拓扑可以相对地用于推断非模式生物的局部网络结构。高局部聚集性是相互作用可靠性的标准，符合优先进化保守和显着共表达。这些强烈而稳定的相关性表明，进化单位超越了单一蛋白质，包括了它们之间的相互作用。特别是，这些信号在极端噪声面前的稳定性表明，经验蛋白质相互作用数据可以与围绕这些蛋白质相互作用的同源聚类相结合，以可靠地推断非模式生物中的局部网络结构。
The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-protein interaction data casts doubt on the broader usefulness of these interaction sets. Approaches focusing on one-protein-at-a-time have been powerfully employed to demonstrate the high degree of conservation of proteins participating in numerous interactions; here, we expand his 'node' focused paradigm to investigate the relative persistence of 'link' based evolutionary signals in a protein interaction network of S. cerevisiae and point out the value of this relatively untapped source of information. The trend for highly connected proteins to be preferably conserved in evolution is stable, even in the context of tremendous noise in the underlying protein interactions as well as in the assignment of orthology among five higher eukaryotes. We find that local clustering around interactions correlates with preferred evolutionary conservation of the participating proteins; furthermore the correlation between high local clustering and evolutionary conservation is accompanied by a stable elevated degree of coexpression of the interacting proteins. We use this conserved interaction data, combined with P. falciparum /Yeast orthologs, as proof-of-principle that high-order network topology can be used comparatively to deduce local network structure in non-model organisms. High local clustering is a criterion for the reliability of an interaction and coincides with preferred evolutionary conservation and significant coexpression. These strong and stable correlations indicate that evolutionary units go beyond a single protein to include the interactions among them. In particular, the stability of these signals in the face of extreme noise suggests that empirical protein interaction data can be integrated with orthologous clustering around these protein interactions to reliably infer local network structures in non-model organisms.
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影响因子：
9.8
作者：
Bozdech, Zbynek;Llinas, Manuel;Pulliam, Brian Lee;Wong, Edith D;Zhu, Jingchun;DeRisi, Joseph L
通讯作者：
DeRisi, Joseph L
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
影响因子：
64.8
作者：
Jeong, H;Mason, SP;Oltvai, ZN
通讯作者：
Oltvai, ZN
影响因子：
64.8
作者：
Rain, JC;Selig, L;Legrain, P
通讯作者：
Legrain, P
DOI：
10.1073/pnas.0409522102
发表时间：
2005-02-08
影响因子：
11.1
作者：
Sharan, R;Suthram, S;Ideker, T
通讯作者：
Ideker, T