Phylogenetic profiling of Arabidopsis genes by monitoring spatial gene expression using cDNA microarrays

Arabidopsis cDNA microarray analysis was performed for 5,722 genes using leaf, stem, root and flower mRNA as targets. We identified 55, 22, 21, and 131 genes expressed specifically in leaves, stems, flowers and roots, respectively. Statistical cluster analysis revealed that the roots were the most distant and the leaves and flowers the most related organs with regards to gene expression. K-means clustering revealed that the clusters for leaf-specific genes tended to mainly have genes for plastid-localized proteins, while the cluster for predominantly root-specific genes was mainly secretory proteins.