Root transcriptome profiles of Rorippa species using Arabidopsis gene chips. A, Numbers of genes regulated by submergence treatment and overlap between species. Within each genotype, expression values of submergence-induced genes show a ratio of submerged to air of greater than 2.0, and submergence-repressed genes show a ratio of submerged to air of less than 0.5 with a significant treatment effect (FDR < 0.05; t test with multiple testing correction according to Benjamini and Hochberg, 1995). B, Results of PCA applied to the expression of all the genes represented on the microarray. A probe mask with a threshold of 80 was applied to the expression data. For each of the 12 microarrays, expression data of 21,288 genes were used as input.