Oscillatory and anti-oscillatory motifs in genetic regulatory networks

doi:10.1088/1674-1056/21/6/060203

中国物理B ›› 2012, Vol. 21 ›› Issue (6): 60203-060203.doi: 10.1088/1674-1056/21/6/060203

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

叶纬明^a, 张朝阳^b, 吕彬彬^c, 狄增如^a, 胡岗^b

a. Department of Systems Science, School of Management and Center for Complexity Research, Beijing Normal University, Beijing 100875, China;
b. Department of Physics, Beijing Normal University, Beijing 100875, China;
c. General Research Institute for Nonferrous Metals, and Grirem Advanced Materials Co. Ltd., Beijing 100088, China

收稿日期:2011-12-21 修回日期:2012-02-17 出版日期:2012-05-01 发布日期:2012-05-01
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 10975015) and the National Basic Research Program of China (Grant No. 2007CB814800).

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

Ye Wei-Ming(叶纬明)^a), Zhang Zhao-Yang(张朝阳)^b), LŰ Bin-Bin(吕彬彬)^c), Di Zeng-Ru(狄增如)^a), and Hu Gang(胡岗)^b)†

a. Department of Systems Science, School of Management and Center for Complexity Research, Beijing Normal University, Beijing 100875, China;
b. Department of Physics, Beijing Normal University, Beijing 100875, China;
c. General Research Institute for Nonferrous Metals, and Grirem Advanced Materials Co. Ltd., Beijing 100088, China

Received:2011-12-21 Revised:2012-02-17 Online:2012-05-01 Published:2012-05-01
Contact: Hu Gang E-mail:ganghu@bnu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 10975015) and the National Basic Research Program of China (Grant No. 2007CB814800).

摘要/Abstract

摘要： Recently, self-sustained oscillatory genetic regulatory networks (GRNs) have attracted significant attention in the biological field. Given a GRN, it is important to anticipate whether the network could generate oscillation with proper parameters, and what the key ingredients for the oscillation are. In this paper the ranges of some function-related parameters which are favorable to sustained oscillations are considered. In particular, some oscillatory motifs appearing with high-frequency in most of the oscillatory GRNs are observed. Moreover, there are some anti-oscillatory motifs which have a strong oscillation repressing effect. Some conclusions analyzing these motif effects and constructing oscillatory GRNs are provided.

关键词: genetic regulatory network, oscillatory motif, anti-oscillatory motif, feedback loop

Abstract: Recently, self-sustained oscillatory genetic regulatory networks (GRNs) have attracted significant attention in the biological field. Given a GRN, it is important to anticipate whether the network could generate oscillation with proper parameters, and what the key ingredients for the oscillation are. In this paper the ranges of some function-related parameters which are favorable to sustained oscillations are considered. In particular, some oscillatory motifs appearing with high-frequency in most of the oscillatory GRNs are observed. Moreover, there are some anti-oscillatory motifs which have a strong oscillation repressing effect. Some conclusions analyzing these motif effects and constructing oscillatory GRNs are provided.

Key words: genetic regulatory network, oscillatory motif, anti-oscillatory motif, feedback loop

中图分类号: (Numerical simulation; solution of equations)

02.60.Cb

05.65.+b (Self-organized systems) 87.15.A- (Theory, modeling, and computer simulation) 87.18.Cf (Genetic switches and networks)

叶纬明, 张朝阳, 吕彬彬, 狄增如, 胡岗. Oscillatory and anti-oscillatory motifs in genetic regulatory networks[J]. 中国物理B, 2012, 21(6): 60203-060203.

Ye Wei-Ming(叶纬明), Zhang Zhao-Yang(张朝阳), LŰ Bin-Bin(吕彬彬), Di Zeng-Ru(狄增如), and Hu Gang(胡岗) . Oscillatory and anti-oscillatory motifs in genetic regulatory networks[J]. Chin. Phys. B, 2012, 21(6): 60203-060203.

参考文献 28

[1]	Tavazoie S, Hughes J D, Campbell M J, Cho R J and Church G M 1999 Nat. Genet. 22 281
[2]	Xu P X, Zhang X, Heaney S, Yoon A, Michelson A M and Maas R L 1999 Development 126 383
[3]	Peterson K J and Davidson E H 2000 PNAS USA 97 4430
[4]	Lee T I, Rinaldi N J, Robert F, Odom D T, Bar-Joseph Z, et al. 2002 Science 298 799
[5]	Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y and Barkai N 2002 Nat. Genet. 31 370
[6]	Ma H W, Kumar B, Ditges U, Gunzer F, Buer J and Zeng A P 2004 Nucleic Acids Res. 32 6643
[7]	Posfai G, Plunkett III G, et al. 2006 Science 312 1044
[8]	Gilchrist M, Thorsson V, Li B, Rust A G, Korb M, Kennnedy K, Hai T, Bolouri H and Aderem A 2006 Nature 441 173
[9]	Kurland C G, Collins L J and Penny D 2006 Science 312 1011
[10]	McAdams H H, Srinivasan B and Arkin A P 2004 Nature Rev. Genet. 5 1
[11]	Shen-Orr S S, Milo R, Mangan S and Alon U 2002 Nat. Gent. 31 64
[12]	Thomas R and Kaufman M 2001 Chaos 11 180
[13]	Snoussi E H 1998 J. Biol. Sys. 6 3
[14]	Plahte E H, Mestl T and Omholt W S 1995 J. Biol. Sys. 3 409
[15]	Pomerening J R, Kim S Y and Ferrell J E 2005 Cell 122 565
[16]	Elowitz M B and Leibler S 2000 Nature 403 335
[17]	Goh K G, Kahng B and Cho K H 2008 Biophys. J. 94 4270
[18]	Tsai T Y C, Choi Y S, Ma W Z, Pomerening J R, Chao T and Ferrell J E 2008 Science 321 126
[19]	Angeli D, Ferrell J E and Sontag E D 2004 PNAS 101 1822
[20]	Ye W M, Huang X D, Huang X H, Li P F, Xia Q Z and Hu G 2010 Phys. Lett. A 374 2521
[21]	Nochomovitz Y D and Li H 2005 PNAS 103 4180
[22]	Gonze D 2010 Biosystems 99 60
[23]	Perkins T J, Hallett M and Glass L 2004 J. Theor. Bio. 230 289
[24]	Qian Y, Liao X H, Huang X D and Hu G 2010 Phys. Rev. E 81 036101
[25]	Liao X H et al. 2011 Front. Phys. 6 124
[26]	Liao X H et al. 2009 arXiv/: 0906.2356
[27]	Lipshtat A, Purushothaman S P, Lyengar R and Maayan A 2008 Biophys. J. 94 2566
[28]	Kim J R, Yoon Y and Cho K H 2008 Biophys. J. 94 359

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

Oscillatory and anti-oscillatory motifs in genetic regulatory networks

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献 28

相关文章 3

Metrics

本文评价

推荐阅读 0

[1]	张益, 叶文军, 袁萍, 朱铧丞, 杨阳, 黄卡玛. Analysis and experiments of self-injection magnetron[J]. 中国物理B, 2016, 25(4): 48402-048402.
[2]	林鹏, 秦开宇, 吴海燕. Stability of piecewise-linear models of genetic regulatory networks[J]. 中国物理B, 2011, 20(10): 108701-108701.
[3]	李莹, 刘曾荣, 张建宝. Dynamics of network motifs in genetic regulatory networks[J]. 中国物理B, 2007, 16(9): 2587-2594.