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Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Biology .
Center for BioDynamics, Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States.
Center for BioDynamics, Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States, Department of Bioengineering, Univ. of California at San Diego, San Diego, CA 92093-0412, United States.
Center for BioDynamics, Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States.
2003 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 100, no 10, 5944-5949 p.Article in journal (Refereed) Published
Abstract [en]

While the fundamental building blocks of biology are being tabulated by the various genome projects, microarray technology is setting the stage for the task of deducing the connectivity of large-scale gene networks. We show how the perturbation of carefully chosen genes in a microarray experiment can be used in conjunction with a reverse engineering algorithm to reveal the architecture of an underlying gene regulatory network. Our iterative scheme identifies the network topology by analyzing the steady-state changes in gene expression resulting from the systematic perturbation of a particular node in the network. We highlight the validity of our reverse engineering approach through the successful deduction of the topology of a linear in numero gene network and a recently reported model for the segmentation polarity network in Drosophila melanogaster. Our method may prove useful in identifying and validating specific drug targets and in deconvolving the effects of chemical compounds.

Place, publisher, year, edition, pages
2003. Vol. 100, no 10, 5944-5949 p.
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-46635DOI: 10.1073/pnas.0933416100OAI: oai:DiVA.org:liu-46635DiVA: diva2:267531
Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-13

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Tegnér, Jesper

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