Bioinformatics Vol. 19 no. 9 2003
Pages 1140-1146
© 2003 Oxford University Press
eXPatGen: generating dynamic expression patterns for the systematic evaluation of analytical methods
1 Department of Chemical Engineering, University
of Delaware, Newark, DE 19716, USA
2 College of
Marine Studies, University of Delaware, Lewes, DE 19958,
USA
Received on April 30, 2002
; revised on August 27, 2002
; accepted on December 28, 2002
Motivation: Experimental gene expression data sets, such as those generated by microarray or gene chip experiments, typically have significant noise and complicated interconnectivities that make understanding even simple regulatory patterns difficult. Given these complications, characterizing the effectiveness of different analysis techniques to uncover network groups and structures remains a challenge. Generating simulated expression patterns with known biological features of expression complexity, diversity and interconnectivities provides a more controlled means of investigating the appropriateness of different analysis methods. A simulation-based approach can systematically evaluate different gene expression analysis techniques and provide a basis for improved methods in dynamic metabolic network reconstruction
Results: We have developed an on-line simulator, called eXPatGen, to generate dynamic gene expression patterns typical of microarray experiments. eXPatGen provides a quantitative network structure to represent key biological features, including the induction, repression, and cascade regulation of messenger RNA (mRNA). The simulation is modular such that the expression model can be replaced with other representations, depending on the level of biological detail required by the user. Two example gene networks, of 25 and 100 genes respectively, were simulated. Two standard analysis techniques, clustering and PCA analysis, were performed on the resulting expression patterns in order to demonstrate how the simulator might be used to evaluate different analysis methods and provide experimental guidance for biological studies of gene expression
Availability: http://www.che.udel.edu/eXPatGen/
Contact: dhurjati{at}che.udel.edu
* To whom correspondence should be addressed.
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