Graph theoretic analysis of protein interaction networks of eukaryotes
Graph theoretic analysis of protein interaction networks of eukaryotes
复制标题
真核生物蛋白质相互作用网络的图论分析
DOI：
10.1016/j.physa.2005.03.044
复制
发表时间：
2005
影响因子：
3.3
通讯作者：
Dong Chul Kim
中科院分区：
文献类型：
--
作者：
Kwang;B. Kahng;Dong Chul Kim
由于高通量实验技术的最新进展，对典型多细胞物种、线虫秀丽隐杆线虫和果蝇果蝇的大规模蛋白质相互作用数据集进行了分析。数据集主要通过酵母混合方法获得，该方法同时包含假阳性和假阴性。因此，虽然需要通过进一步的湿实验来测试此类数据集，但在这里我们引用最近开发的网络理论以简单的方式测试此类高通量数据集。基于维持生命所必需的关键生物过程在真核物种中是保守的这一事实，以及将两个物种的蛋白质相互作用网络（PIN）的结构特性与酵母PIN的结构特性进行比较，我们发现，虽然蠕虫和酵母PIN数据集表现出相似的结构特性，但当前的果蝇数据集虽然经过了最全面的筛选，但并不能正确地反映通用结构特性。模块化被抑制，连通性相关性缺失。在当前的飞行数据集中添加 interologs 增加了模块性并增强了三角形图案的出现。然而，在这种内源性添加下，果蝇的连接相关函数仍然不同，为此我们通过计算机建模提出了一个可能的场景。
Owing to the recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high-throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are conserved across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interologs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interolog additions, for which we present a possible scenario through an in silico modeling.
影响因子：
64.8
作者：
Uetz, P;Giot, L;Rothberg, JM
通讯作者：
Rothberg, JM
DOI：
10.1073/pnas.061034498
发表时间：
2001-04-10
影响因子：
11.1
作者：
Ito, T;Chiba, T;Sakaki, Y
通讯作者：
Sakaki, Y