Effective Models of Periodically Driven Networks

Circadian rhythms are governed by a highly coupled, complex network of genes. Due to feedback within the network, any modification of the system's state requires coherent changes in several nodes. A model of the underlying network is necessary to compute these modifications. We use an effective...

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Bibliographic Details
Published in:Biophysical journal 2011-12, Vol.101 (11), p.2563-2571
Main Authors: Shulman, Jason, Seemann, Lars, Gunaratne, Gemunu H.
Format: Article
Language:English
Subjects:
Animals
Biological Systems and Multicellular Dynamics
Circadian rhythm
Circadian Rhythm - genetics
Circadian Rhythm - physiology
Gene expression
Gene Expression Regulation
Gene Knockout Techniques
Gene Regulatory Networks - genetics
Genes
Heart
Mammals
Mammals - genetics
Mammals - physiology
microarray technology
Models, Genetic
mutants
Mutation
Mutation - genetics
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Summary:Circadian rhythms are governed by a highly coupled, complex network of genes. Due to feedback within the network, any modification of the system's state requires coherent changes in several nodes. A model of the underlying network is necessary to compute these modifications. We use an effective modeling approach for this task. Rather than inferred biochemical interactions, our method utilizes microarray data from a group of mutants for its construction. With simulated data, we develop an effective model for a circadian network in a peripheral tissue, subject to driving by the suprachiasmatic nucleus, the mammalian pacemaker. The effective network can predict time-dependent gene expression levels in other mutants.
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2011.10.008