Sharan Roded, Ideker Trey
School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
Nat Biotechnol. 2006 Apr;24(4):427-33. doi: 10.1038/nbt1196.
Molecular networks represent the backbone of molecular activity within the cell. Recent studies have taken a comparative approach toward interpreting these networks, contrasting networks of different species and molecular types, and under varying conditions. In this review, we survey the field of comparative biological network analysis and describe its applications to elucidate cellular machinery and to predict protein function and interaction. We highlight the open problems in the field as well as propose some initial mathematical formulations for addressing them. Many of the methodological and conceptual advances that were important for sequence comparison will likely also be important at the network level, including improved search algorithms, techniques for multiple alignment, evolutionary models for similarity scoring and better integration with public databases.
分子网络代表了细胞内分子活动的主干。最近的研究采用了一种比较方法来解释这些网络，对比不同物种、分子类型以及在不同条件下的网络。在本综述中，我们概述了比较生物网络分析领域，并描述了其在阐明细胞机制、预测蛋白质功能和相互作用方面的应用。我们强调了该领域的开放性问题，并提出了一些初步的数学公式来解决这些问题。许多对序列比较很重要的方法和概念进展在网络层面可能也很重要，包括改进的搜索算法、多序列比对技术、相似性评分的进化模型以及与公共数据库的更好整合。
