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In Silico Biology 5, 0023 (2005); ©2005, Bioinformation Systems e.V.  



Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks

Angelica Lindlöf1,* and Zelmina Lubovac1,*

1University of Skövde, Box 408, 541 28 Skövde, Sweden

* Corresponding authors; Email: angelica@ida.his.sezelmina@ida.his.se


Edited by H. Michael; received August 06, 2004; revised and accepted January 21, 2005; published February 16, 2005


Abstract

Recent research on large scale microarray analysis has explored the use of Relevance Networks to find networks of genes that are associated to each other in gene expression data. In this work, we compare Relevance Networks with other types of clustering methods to test some of the stated advantages of this method. The dataset we used consists of artificial time series of Boolean gene expression values, with the aim of mimicking microarray data, generated from simple artificial genetic networks. By using this dataset, we could not confirm that Relevance Networks based on mutual information perform better than Relevance Networks based on Pearson correlation, partitional clustering or hierarchical clustering, since the results from all methods were very similar. However, all three methods successfully revealed the subsets of co-expressed genes, which is a valuable step in identifying co-regulation.

Keywords: Relevance Networks, clustering, regulatory networks, microarray data analysis, simulation