Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
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DOI：
10.1002/pmic.200600636
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发表时间：
2007-03-01
期刊：
影响因子：
3.4
通讯作者：
Wodak, Shoshana J.
中科院分区：
文献类型：
--
作者：
Pu, Shuye;Vlasblom, Jim;Wodak, Shoshana J.
关于基因产物之间物理和功能相互作用的可靠信息是得出有意义的细胞过程的系统级描述的重要先决条件。最近，通过两个全面的串联亲和纯化/质谱学(TAP/MS)研究，关于酿酒酵母中蛋白质相互作用的可用信息已经大大增加。然而，使用略有不同的方法，这些研究产生了对酵母相互作用组的不同描述，清楚地说明了这样一个事实，即将纯化数据转换为准确的蛋白质-蛋白质相互作用和复合体仍然是一个主要挑战。在这里，我们回顾了这一过程中涉及的主要分析步骤，特别关注从二元相互作用网络中推导出络合物的任务。将马尔可夫聚类法应用于一个可供选择的酵母相互作用网络，结合最近两个最新的TAP/MS研究的数据，我们产生了对酵母蛋白复合体的新描述。几个客观标准表明，这一新的描述比以前发表的描述更准确、更有意义。同样的标准也被用来衡量推导二元相互作用和络合物的不同方法可能对结果产生的影响。最后，研究表明，使用相同的过程来处理最新的纯化数据集显著地提高了所得到的交互组描述之间的收敛。
Reliable information on the physical and functional interactions between the gene products is an important prerequisite for deriving meaningful system-level descriptions of cellular processes. The available information about protein interactions in Saccharomyces cerevisiae has been vastly increased recently by two comprehensive tandem affinity purification/mass spectrometry (TAP/MS) studies. However, using somewhat different approaches, these studies produced diverging descriptions of the yeast interactome, clearly illustrating the fact that converting the purification data into accurate sets of protein-protein interactions and complexes remains a major challenge. Here, we review the major analytical steps involved in this process, with special focus on the task of deriving complexes from the network of binary interactions. Applying the Markov Cluster procedure to an alternative yeast interaction network, recently derived by combining the data from the two latest TAP/MS studies, we produce a new description of yeast protein complexes. Several objective criteria suggest that this new description is more accurate and meaningful than those previously published. The same criteria are also used to gauge the influence that different methods for deriving binary interactions and complexes may have on the results. Lastly, it is shown that employing identical procedures to process the latest purification datasets significantly improves the convergence between the resulting interactome descriptions.