Finding large domains of similarly expressed genes

Abstract

In this study, a new method for finding and defining large domains of adjacent genes on a chromosome with similar expression profiles was introduced based on the use of the minimum description length (MDL) principle and the recursive segmentation procedure. For the recursive segmentation, a newly introduced stopping criterion using the MDL principle was used. Together they offer a novel method to view the large domains of similarly expressed genes in genome data. The description of the genome data and of the large domain is done according to the MDL principle, which selects the model based on its fitting performance and also penalized a very high complexity of the model. The success of segmentation comes from observation that the more similar the gene expression profiles are in a large domain, the shorter the description of the data that represents the large domain. The new recursive segmentation method was applied to the microarray measurements of the Drosophila genome and human genome in order to demonstrate the ability of the new method to find large domains successfully.