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Experiment Design for Proper Excitation of Gene Regulatory Networks
KTH, School of Electrical Engineering (EES), Automatic Control.
KTH, School of Electrical Engineering (EES), Automatic Control.
2007 (English)In: Proceedings of Foundations of Systems Biology in Engineering (FOSBE), 2nd Conference, 2007Conference paper (Refereed)
Abstract [en]

Feedback is ubiquitous in gene regulatory networks, and provide e.g., homeostasis and signal amplification. The presence of feedback has significant implications for network inference since it implies that the gene responses to perturbation experiments typically will be strongly correlated, leading to ill-conditioning of the measurement matrix. The ill-conditioning will represent a fundamental problem in network identification since it implies that some of the network interactions will be identified with gross errors. To overcome this problem, we propose herein a systematic iterative experiment design that ensures sufficient excitations of all network interactions. The method leads to combinatorial perturbation experiments, in which a number of genes are perturbed simultaneously. The effectiveness of the method is demonstrated by application to an in silico regulatory network.

Place, publisher, year, edition, pages
Keyword [en]
Experiment design, Gene regulatory networks, Network inference, Perturbation experiments, Reverse engineering, System identification
National Category
Bioinformatics and Systems Biology Control Engineering
URN: urn:nbn:se:kth:diva-80749OAI: diva2:496816
2nd Foundations of Systems Biology in Engineering (FOSBE). Stuttgart, Germany. September 9 - 12, 2007
QC 20120515Available from: 2012-02-10 Created: 2012-02-10 Last updated: 2012-05-15Bibliographically approved

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Nordling, Torbjörn E. M.Jacobsen, Elling W.
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