cis element analysis using DNA array data in Arabidopsis

Abstract

Although cis element prediction from gene expression data is generally used, there are few reports in plant science for a comprehensive analysis of regulatory mechanisms of gene expression using bioinformatics approach. We comprehensively predicted cis elements from gene expression data obtained by microarray. Based on the results of cis element prediction, we estimated regulatory mechanisms of gene expression by computational analysis. As an example of estimation of regulatory mechanisms, genes for ribosome proteins will be presented.
<Flow of analysis>
1. classify genes using gene expression data
2. extract conserved sequences from promoter regions of the gene groups
3. evaluate effects of the conserved sequences on gene expression
4. extract non-redundant cis elements
5. assess the cis element predictions
6. estimate regulatory mechanisms of gene expression