Generic properties of random gene regulatory networks

Abstract

Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In particular, it is not clear typically how attractors partition among the three types of orbits: steady state, periodic and chaotic, and how the dynamical properties change with network’s topological characteristics. In this work, we first investigated these questions in random GRNs with different network sizes, connectivity, fraction of inhibitory links and transcription regulation rules. Then we searched for the core motifs that govern the dynamic behavior of large GRNs. We show that the stability of a random GRN is typically governed by a few embedding motifs of small sizes, and therefore can in general be understood in the context of these short motifs. Our results provide insights for the study and design of genetic networks.

Keywords

genetic network / dynamic attractors / complex systems

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ACKNOWLEDGEMENTS

This work was supported in part by NSF (DMR-0804183; CMMI-0941355), NIH (R01 GM097115; P50 GM081879), MOST (2009CB918500) and National Natural Science Foundation of China. We thank Leon Glass and Gang Hu for helpful discussions.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Zhiyuan Li, Simone Bianco, Zhaoyang Zhang and Chao Tang declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg