Suppr超能文献

细胞网络中模块化的自发出现。

Spontaneous emergence of modularity in cellular networks.

作者信息

Solé Ricard V, Valverde Sergi

机构信息

Complex Systems Lab, ICREA-UPF, Dr Aiguader 88, 08003 Barcelona, Spain.

出版信息

J R Soc Interface. 2008 Jan 6;5(18):129-33. doi: 10.1098/rsif.2007.1108.

Abstract

Modularity is known to be one of the most relevant characteristics of biological systems and appears to be present at multiple scales. Given its adaptive potential, it is often assumed to be the target of selective pressures. Under such interpretation, selection would be actively favouring the formation of modular structures, which would specialize in different functions. Here we show that, within the context of cellular networks, no such selection pressure is needed to obtain modularity. Instead, the intrinsic dynamics of network growth by duplication and diversification is able to generate it for free and explain the statistical features exhibited by small subgraphs. The implications for the evolution and evolvability of both biological and technological systems are discussed.

摘要

模块化是生物系统最相关的特征之一,且似乎存在于多个尺度。鉴于其适应潜力,人们通常认为它是选择压力的目标。在这种解释下,选择会积极促进模块化结构的形成,这些结构将专门执行不同的功能。在这里我们表明,在细胞网络的背景下,获得模块化不需要这样的选择压力。相反,通过复制和多样化实现的网络增长的内在动力学能够免费生成模块化,并解释小子图所展现的统计特征。本文还讨论了这对生物和技术系统的进化及演化能力的影响。

相似文献

1
Spontaneous emergence of modularity in cellular networks.
J R Soc Interface. 2008 Jan 6;5(18):129-33. doi: 10.1098/rsif.2007.1108.
2
Breakdown of Modularity in Complex Networks.
Front Physiol. 2017 Jul 13;8:497. doi: 10.3389/fphys.2017.00497. eCollection 2017.
3
The evolutionary origins of modularity.
Proc Biol Sci. 2013 Jan 30;280(1755):20122863. doi: 10.1098/rspb.2012.2863. Print 2013 Mar 22.
4
Modularity, evolvability, and adaptive radiations: a comparison of the hemi- and holometabolous insects.
Evol Dev. 2001 Mar-Apr;3(2):59-72. doi: 10.1046/j.1525-142x.2001.003002059.x.
5
Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability.
PLoS Comput Biol. 2011 Oct;7(10):e1002208. doi: 10.1371/journal.pcbi.1002208. Epub 2011 Oct 6.
6
Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Phys Biol. 2013 Aug;10(4):040301. doi: 10.1088/1478-3975/10/4/040301. Epub 2013 Aug 2.
7
Modularity and anti-modularity in networks with arbitrary degree distribution.
Biol Direct. 2010 May 6;5:32. doi: 10.1186/1745-6150-5-32.
8
Is evolvability involved in the origin of modular variation?
Evolution. 2003 Jun;57(6):1448-50. doi: 10.1111/j.0014-3820.2003.tb00352.x.
9
Convergent evolution of modularity in metabolic networks through different community structures.
BMC Evol Biol. 2012 Sep 14;12:181. doi: 10.1186/1471-2148-12-181.
10
Topology of biological networks and reliability of information processing.
Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18414-9. doi: 10.1073/pnas.0509132102. Epub 2005 Dec 8.

引用本文的文献

1
Life's building blocks: the modular path to multiscale complexity.
Front Syst Biol. 2024 Jul 17;4:1417800. doi: 10.3389/fsysb.2024.1417800. eCollection 2024.
3
Mechanistic interactions as the origin of modularity in biological networks.
Proc Biol Sci. 2024 Apr 30;291(2021):20240269. doi: 10.1098/rspb.2024.0269. Epub 2024 Apr 17.
4
Composition, structure and robustness of Lichen guilds.
Sci Rep. 2023 Feb 25;13(1):3295. doi: 10.1038/s41598-023-30357-w.
5
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks.
BMC Bioinformatics. 2022 Nov 28;23(1):509. doi: 10.1186/s12859-022-05067-1.
7
Intrinsic limitations in mainstream methods of identifying network motifs in biology.
BMC Bioinformatics. 2020 Apr 29;21(1):165. doi: 10.1186/s12859-020-3441-x.
8
Evolving complexity: how tinkering shapes cells, software and ecological networks.
Philos Trans R Soc Lond B Biol Sci. 2020 Apr 13;375(1796):20190325. doi: 10.1098/rstb.2019.0325. Epub 2020 Feb 24.
9
Disconnected, fragmented, or united? a trans-disciplinary review of network science.
Appl Netw Sci. 2016;1(1):6. doi: 10.1007/s41109-016-0010-3. Epub 2016 Jul 20.
10
Ecological and evolutionary dynamics of interconnectedness and modularity.
Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):750-755. doi: 10.1073/pnas.1716078115. Epub 2018 Jan 8.

本文引用的文献

1
Statistical mechanics of community detection.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jul;74(1 Pt 2):016110. doi: 10.1103/PhysRevE.74.016110. Epub 2006 Jul 18.
2
Are network motifs the spandrels of cellular complexity?
Trends Ecol Evol. 2006 Aug;21(8):419-22. doi: 10.1016/j.tree.2006.05.013. Epub 2006 Jun 9.
3
Modularity and community structure in networks.
Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8577-82. doi: 10.1073/pnas.0601602103. Epub 2006 May 24.
5
Network growth models and genetic regulatory networks.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031912. doi: 10.1103/PhysRevE.73.031912. Epub 2006 Mar 14.
6
Topology of biological networks and reliability of information processing.
Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18414-9. doi: 10.1073/pnas.0509132102. Epub 2005 Dec 8.
7
Topology, tinkering and evolution of the human transcription factor network.
FEBS J. 2005 Dec;272(24):6423-34. doi: 10.1111/j.1742-4658.2005.05041.x.
8
Network motifs in computational graphs: a case study in software architecture.
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug;72(2 Pt 2):026107. doi: 10.1103/PhysRevE.72.026107. Epub 2005 Aug 8.
9
Spontaneous evolution of modularity and network motifs.
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13773-8. doi: 10.1073/pnas.0503610102. Epub 2005 Sep 20.
10
Duplication-divergence model of protein interaction network.
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jun;71(6 Pt 1):061911. doi: 10.1103/PhysRevE.71.061911. Epub 2005 Jun 22.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验