HCL analysis of candidate genes showing significant differential expression patterns after submergence. The left panel displays log₂ fold ratios from seven comparisons, and the right panel represents log₂-transformed normalized intensity in six samples used for this microarray experiment of each probe. Red indicates up-regulation in M202(Sub1) compared with M202 after submergence, in M202(Sub1) after submergence compared with before submergence, and in M202 after submergence compared with before submergence, and green indicates down-regulation for the same comparisons. Blue indicates background level of expression, and yellow indicates high level of expression. Various colored boxes indicate clusters showing similar tendencies of gene expression. Later, clusters 1, 2, 3, 6, 7, 8, and 9 were applied for Figure 6 and Supplemental Figure S3, and clusters 4, 5, 10, and 11 were applied for Supplemental Figures S5 and S6. S/M_0 d, Log₂ ratio of M202(Sub1) compared with M202 before submergence; S/M_1 d, log₂ ratio of M202(Sub1) compared with M202 at 1 d after submergence; S/M_6 d, log₂ ratio of M202(Sub1) compared with M202 at 6 d after submergence; 1 d/0 d_S, log₂ ratio of M202(Sub1) at 1 d after submergence compared with before submergence; 6 d/0 d_S, log₂ ratio of M202(Sub1) at 6 d after submergence compared with before submergence; 1 d/0 d_M, log₂ ratio of M202 at 1 d after submergence compared with before submergence; 6 d/0 d_M, log₂ ratio of M202 at 6 d after submergence compared with before submergence. The blue-yellow bar indicates log₂-transformed normalized expression levels of Affymetrix and NSF45K array data, and the range is from 14 to 6. The green-red bar indicates fold change values of seven comparisons in NSF45K array data, and the range is from −2 to 2. [See online article for color version of this figure.]