The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses
The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses
复制标题
预测的拟南芥互作组资源和基于网络拓扑的系统生物学分析
DOI：
10.1105/tpc.110.082529
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发表时间：
2011-03-01
期刊：
影响因子：
11.6
通讯作者：
Chen, Xin
中科院分区：
文献类型：
--
作者：
Lin, Mingzhi;Zhou, Xi;Chen, Xin
预测的相互作用是分子机制研究中实验报告的相互作用的宝贵补充，特别是对于高等生物，报告的实验相互作用仅占其总相互作用组的一小部分。通过对先前工作的经验教训进行仔细的工程考虑，预测拟南芥互作组资源（PAIR；http://www.cls.zju.edu.cn/pair/）呈现了 149,900 个潜在的分子相互作用，预计涵盖：整个相互作用组的 24%； 40% 的精度。这项研究表明，尽管 PAIR 的覆盖范围仍然有限，但它足够丰富，可以捕获高阶生物系统内部和之间的许多重要功能联系，例如途径和生物过程。这些推断的相互作用可以很好地支持多种基于网络拓扑的系统生物学分析，例如基因集连锁分析、蛋白质功能预测以及显示不显着表达变化的调控基因的识别。 PAIR 中大幅扩展的分子网络大大提高了这些分析的能力，以整合现有知识，并对基因和基因网络的功能和协调提出新的见解。
Predicted interactions are a valuable complement to experimentally reported interactions in molecular mechanism studies, particularly for higher organisms, for which reported experimental interactions represent only a small fraction of their total interactomes. With careful engineering consideration of the lessons from previous efforts, the Predicted Arabidopsis Interactome Resource (PAIR; http://www.cls.zju.edu.cn/pair/) presents 149,900 potential molecular interactions, which are expected to cover; 24% of the entire interactome with; 40% precision. This study demonstrates that, although PAIR still has limited coverage, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes. These inferred interactions can nicely power several network topology-based systems biology analyses, such as gene set linkage analysis, protein function prediction, and identification of regulatory genes demonstrating insignificant expression changes. The drastically expanded molecular network in PAIR has considerably improved the capability of these analyses to integrate existing knowledge and suggest novel insights into the function and coordination of genes and gene networks.