Lima-Mendez Gipsi, van Helden Jacques
Bioinformatique des Génomes et des Réseaux-BiGRe, Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, B-1050 Bruxelles, Belgium.
Mol Biosyst. 2009 Dec;5(12):1482-93. doi: 10.1039/b908681a. Epub 2009 Oct 2.
For almost 10 years, topological analysis of different large-scale biological networks (metabolic reactions, protein interactions, transcriptional regulation) has been highlighting some recurrent properties: power law distribution of degree, scale-freeness, small world, which have been proposed to confer functional advantages such as robustness to environmental changes and tolerance to random mutations. Stochastic generative models inspired different scenarios to explain the growth of interaction networks during evolution. The power law and the associated properties appeared so ubiquitous in complex networks that they were qualified as "universal laws". However, these properties are no longer observed when the data are subjected to statistical tests: in most cases, the data do not fit the expected theoretical models, and the cases of good fitting merely result from sampling artefacts or improper data representation. The field of network biology seems to be founded on a series of myths, i.e. widely believed but false ideas. The weaknesses of these foundations should however not be considered as a failure for the entire domain. Network analysis provides a powerful frame for understanding the function and evolution of biological processes, provided it is brought to an appropriate level of description, by focussing on smaller functional modules and establishing the link between their topological properties and their dynamical behaviour.
近十年来,对不同大规模生物网络(代谢反应、蛋白质相互作用、转录调控)的拓扑分析一直凸显出一些反复出现的特性:度的幂律分布、无标度性、小世界特性,这些特性被认为赋予了诸如对环境变化的稳健性和对随机突变的耐受性等功能优势。随机生成模型激发了不同的情景来解释进化过程中相互作用网络的增长。幂律及相关特性在复杂网络中似乎极为普遍,以至于它们被称作“普遍规律”。然而,当对数据进行统计检验时,这些特性就不再被观察到:在大多数情况下,数据并不符合预期的理论模型,而拟合良好的情况仅仅是由抽样假象或不当的数据表示导致的。网络生物学领域似乎建立在一系列神话之上,即广泛相信但却是错误的观念。然而,这些基础的弱点不应被视为整个领域的失败。网络分析为理解生物过程的功能和进化提供了一个强大的框架,前提是通过关注较小的功能模块并建立其拓扑特性与其动态行为之间的联系,将其提升到适当的描述水平。