Yook Soon-Hyung, Oltvai Zoltán N, Barabási Albert-László
Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA.
Proteomics. 2004 Apr;4(4):928-42. doi: 10.1002/pmic.200300636.
The elucidation of the cell's large-scale organization is a primary challenge for post-genomic biology, and understanding the structure of protein interaction networks offers an important starting point for such studies. We compare four available databases that approximate the protein interaction network of the yeast, Saccharomyces cerevisiae, aiming to uncover the network's generic large-scale properties and the impact of the proteins' function and cellular localization on the network topology. We show how each database supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong correlations between the network's structure and the functional role and subcellular localization of its protein constituents, concluding that most functional and/or localization classes appear as relatively segregated subnetworks of the full protein interaction network. The uncovered systematic differences between the four protein interaction databases reflect their relative coverage for different functional and localization classes and provide a guide for their utility in various bioinformatics studies.
阐明细胞的大规模组织是后基因组生物学面临的主要挑战，而了解蛋白质相互作用网络的结构为此类研究提供了重要的起点。我们比较了四个近似酿酒酵母蛋白质相互作用网络的现有数据库，旨在揭示该网络的一般大规模特性以及蛋白质功能和细胞定位对网络拓扑结构的影响。我们展示了每个数据库如何支持具有层次模块化的无标度拓扑结构，这表明这些特征代表了蛋白质相互作用网络的稳健且通用的属性。我们还发现网络结构与其蛋白质成分的功能作用和亚细胞定位之间存在强相关性，得出的结论是，大多数功能和/或定位类别表现为完整蛋白质相互作用网络中相对隔离的子网。四个蛋白质相互作用数据库之间发现的系统差异反映了它们对不同功能和定位类别的相对覆盖范围，并为它们在各种生物信息学研究中的效用提供了指导。
