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Proceedings Paper

Genetic network models: a comparative study
Author(s): Eugene P. van Someren; Lodewyk F. A. Wessels; Marcel J. T. Reinders
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Paper Abstract

Currently, the need arises for tools capable of unraveling the functionality of genes based on the analysis of microarray measurements. Modeling genetic interactions by means of genetic network models provides a methodology to infer functional relationships between genes. Although a wide variety of different models have been introduced so far, it remains, in general, unclear what the strengths and weaknesses of each of these approaches are and where these models overlap and differ. This paper compares different genetic modeling approaches that attempt to extract the gene regulation matrix from expression data. A taxonomy of continuous genetic network models is proposed and the following important characteristics are suggested and employed to compare the models: inferential power; predictive power; robustness; consistency; stability and computational cost. Where possible, synthetic time series data are employed to investigate some of these properties. The comparison shows that although genetic network modeling might provide valuable information regarding genetic interactions, current models show disappointing results on simple artificial problems. For now, the simplest models are favored because they generalize better, but more complex models will probably prevail once their bias is more thoroughly understood and their variance is better controlled.

Paper Details

Date Published: 4 June 2001
PDF: 12 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427994
Show Author Affiliations
Eugene P. van Someren, Delft Univ. of Technology (Netherlands)
Lodewyk F. A. Wessels, Delft Univ. of Technology (Netherlands)
Marcel J. T. Reinders, Delft Univ. of Technology (Netherlands)

Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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