基因模块水平分析：网络与动力学的识别
Gene module level analysis: identification to networks and dynamics.
作者信息
Wang Xuewei, Dalkic Ertugrul, Wu Ming, Chan Christina
机构信息
Michigan State University, Chemical Engineering and Materials Science Department, 2527 Engineering building, East Lansing, MI 48823, USA.
出版信息
Curr Opin Biotechnol. 2008 Oct;19(5):482-91. doi: 10.1016/j.copbio.2008.07.011. Epub 2008 Sep 3.
Abstract
Nature exhibits modular design in biological systems. Gene module level analysis is based on this module concept, aiming to understand biological network design and systems behavior in disease and development by emphasizing on modules of genes rather than individual genes. Module level analysis has been extensively applied in genome wide level analysis, exploring the organization of biological systems from identifying modules to reconstructing module networks and analyzing module dynamics. Such module level perspective provides a high level representation of the regulatory scenario and design of biological systems, promising to revolutionize our view of systems biology, genetic engineering as well as disease mechanisms and molecular medicine.
摘要
自然界在生物系统中展现出模块化设计。基因模块水平分析基于这一模块概念，旨在通过强调基因模块而非单个基因来理解疾病和发育过程中的生物网络设计及系统行为。模块水平分析已广泛应用于全基因组水平分析，从识别模块到重建模块网络以及分析模块动态，探索生物系统的组织方式。这种模块水平的视角提供了生物系统调控情况和设计的高层次表示，有望彻底改变我们对系统生物学、基因工程以及疾病机制和分子医学的看法。
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本文引用的文献
1
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BMC Syst Biol. 2008 May 19;2:45. doi: 10.1186/1752-0509-2-45.
2
A modular approach for integrative analysis of large-scale gene-expression and drug-response data.一种用于大规模基因表达和药物反应数据综合分析的模块化方法。
Nat Biotechnol. 2008 May;26(5):531-9. doi: 10.1038/nbt1397.
3
A global pathway crosstalk network.一个全球通路串扰网络。
Bioinformatics. 2008 Jun 15;24(12):1442-7. doi: 10.1093/bioinformatics/btn200. Epub 2008 Apr 23.
4
Protein networks in disease.疾病中的蛋白质网络
Genome Res. 2008 Apr;18(4):644-52. doi: 10.1101/gr.071852.107.
5
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.利用状态空间模型从时间序列基因表达谱进行基于转录模块的基因网络的统计推断。
Bioinformatics. 2008 Apr 1;24(7):932-42. doi: 10.1093/bioinformatics/btm639. Epub 2008 Feb 21.
6
Modeling cancer progression via pathway dependencies.通过通路依赖性对癌症进展进行建模。
PLoS Comput Biol. 2008 Feb;4(2):e28. doi: 10.1371/journal.pcbi.0040028.
7
Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.竞争性和拓扑结构不同的调控模块配对增强了模式化基因表达。
Mol Syst Biol. 2008;4:163. doi: 10.1038/msb.2008.6. Epub 2008 Feb 12.
8
Understanding biological functions through molecular networks.通过分子网络理解生物学功能。
Cell Res. 2008 Feb;18(2):224-37. doi: 10.1038/cr.2008.16.
9
Dynamical pathway analysis.动态通路分析
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10
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