Evaluation of design strategies for time course experiments in genetic networks: the XlnR regulon in Aspergillus niger

J. Omony, A.R. Mach-Aigner, L.H. de Graaff, G. van Straten, A.J.B. van Boxtel

Research output: Chapter in Book/Report/Conference proceedingConference paperAcademic

Abstract

One of the challenges in the reconstruction of genetic network is to find experimental designs that maximize the information content in the data. In this work the information value of time course experiments (TCEs) is used to rank experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, whereby it was the goal to find the best moment to administer an extra pulse of inducing D-xylose. Low and high trigger concentrations are considered. The models that govern the regulation of the target genes in this regulon are used for simulation. Parameter sensitivity analysis, Fisher Information Matrix (FIM) and the E-modified criterion are used for the design performance assessment. The results show that the best time to give a second pulse of a low concentration trigger of D-xylose is when the D-xylose concentration from the first pulse is not yet completed reduced. Secondly, pulses with high trigger concentrations were simulated, parameter sensitivities computed, and the experimental designs evaluated. Overall, after the first pulse of 1 mM D-xylose, using a second pulse of 5 (or 10) mM D-xylose yields the best experimental design - leading to improved parameter estimates
Original languageEnglish
Title of host publicationProceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB "11, Paris, France, 21-23 September 2011
Place of PublicationNew York, NY, USA
PublisherACM
Pages25-33
ISBN (Print)9781450308175
DOIs
Publication statusPublished - 2011
EventCMSB "11, 9th International Conference on computational methods in systems biology, Paris, France -
Duration: 21 Sep 201123 Sep 2011

Conference

ConferenceCMSB "11, 9th International Conference on computational methods in systems biology, Paris, France
Period21/09/1123/09/11

Fingerprint Dive into the research topics of 'Evaluation of design strategies for time course experiments in genetic networks: the XlnR regulon in Aspergillus niger'. Together they form a unique fingerprint.

Cite this