Gene Expression Studies in Arabidopsis thaliana- a Network Perspective

Control at the transcriptional level is the most fundamental mode of regulation of gene expression. Such control can be most effectively studied by monitoring expression patterns of genes in a genome wide fashion using DNA microarrays. In the first part of this chapter, we review some of the gene expression studies, covering tiling arrays and cDNA arrays, of the model flowering plant Arabidopsis thaliana. Following this, we focus on describing different computational methods that one can use to analyze these large-scale gene expression datasets. In this section, after briefly introducing the techniques to cluster genes based on the similarity in expression profiles, we describe a powerful way to analyze this data, which is to study them as networks. Along these lines, we introduce some basic concepts to analyze these networks, describe the topology of simple relevance networks and first-order conditional independence networks. Further more, we also describe methods to derive functional modules from these networks. In conclusion, we explain how these approaches have been applied to gene expression datasets for Arabidopsis thaliana and hope to motivate the reader to think about how the data from plant genomics remains a fertile ground for further studies along similar lines. 1