Cui Guangyu, Shrestha Rojan, Han Kyungsook
School of Computer Science and Engineering, Inha University, Incheon, 402-751, South Korea.
Comput Methods Biomech Biomed Engin. 2012;15(7):691-9. doi: 10.1080/10255842.2011.555404. Epub 2011 Aug 9.
Many biological processes are performed by a group of proteins rather than by individual proteins. Proteins involved in the same biological process often form a densely connected sub-graph in a protein-protein interaction network. Therefore, finding a dense sub-graph provides useful information to predict the function or protein complex of uncharacterised proteins in the sub-graph. We developed a heuristic algorithm that finds functional modules in a protein-protein interaction network and visualises the modules. The algorithm has been implemented in a platform-independent, standalone program called ModuleSearch. In an interaction network of yeast proteins, ModuleSearch found 366 overlapping modules. Of the modules, 71% have a function shared by more than half the proteins in the module and 58% have a function shared by all proteins in the module. Comparison of ModuleSearch with other programs shows that ModuleSearch finds more sub-graphs than most other programs, yet a higher proportion of the sub-graphs correspond to known functional modules. ModuleSearch and sample data are freely available to academics at http://bclab.inha.ac.kr/ModuleSearch.
许多生物学过程是由一组蛋白质而非单个蛋白质执行的。参与同一生物学过程的蛋白质在蛋白质 - 蛋白质相互作用网络中通常会形成一个紧密连接的子图。因此，找到一个密集子图可为预测该子图中未表征蛋白质的功能或蛋白质复合物提供有用信息。我们开发了一种启发式算法，该算法可在蛋白质 - 蛋白质相互作用网络中找到功能模块并将这些模块可视化。该算法已在一个名为ModuleSearch的与平台无关的独立程序中实现。在酵母蛋白质的相互作用网络中，ModuleSearch发现了366个重叠模块。在这些模块中，71% 的模块具有超过一半的蛋白质共享的功能，58% 的模块具有所有蛋白质共享的功能。将ModuleSearch与其他程序进行比较表明，ModuleSearch比大多数其他程序找到的子图更多，而且子图中对应于已知功能模块的比例更高。学者可通过http://bclab.inha.ac.kr/ModuleSearch免费获取ModuleSearch和示例数据。
