Figure 3.

Patterns of variations in transcriptomes and epigenomes between organs and between genotypes. (a,b) Hierarchical clustering of transcription, histone modifications, and DNA-methylation levels in shoots and roots of maize hybrids and their parents. Only genes with significant differences in expression (P<0.001) or epigenetic modifications (P<0.01) in at least one pairwise comparison between organs or between genotypes were clustered using Cluster, version 3.0 (Ward's method, Euclidean distance) and visualized using Java TreeView, version 1.6.6r2. (c) Tree view of hierarchical clustering in (a) and (b). B, B73; M, Mo17; BM, B73 ´ Mo17; MB, Mo17 ´ B73; R, root; S, shoot.