Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks |
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| Authors: | Chushin Koh Fang-Xiang Wu Gopalan Selvaraj Anthony J Kusalik |
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| Affiliation: | 1Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5C9;2Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A9;3Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A9;4Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, SK, Canada, S7N 0W9 |
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| Abstract: | Computational gene regulation models provide a means for scientists to draw biological inferences from time-course gene expression data. Based on the state-space approach, we developed a new modeling tool for inferring gene regulatory networks, called time-delayed Gene Regulatory Networks (tdGRNs). tdGRN takes time-delayed regulatory relationships into consideration when developing the model. In addition, a priori biological knowledge from genome-wide location analysis is incorporated into the structure of the gene regulatory network. tdGRN is evaluated on both an artificial dataset and a published gene expression data set. It not only determines regulatory relationships that are known to exist but also uncovers potential new ones. The results indicate that the proposed tool is effective in inferring gene regulatory relationships with time delay. tdGRN is complementary to existing methods for inferring gene regulatory networks. The novel part of the proposed tool is that it is able to infer time-delayed regulatory relationships. |
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