Figure 4.

Hierarchical clustering of all differentially expressed genes and transcription factor genes in stem internode tissue (IN2 - IN9). Mean centered expression levels are represented with green denoting down regulation, and red indicating upregulation. (A) All 3,016 differentially expressed genes in stem internode tissue (IN2 - IN9). The 3 major clusters of genes with similar expression patterns are marked with vertical lines and numbered 1 to 3. The expression values, gene models, and closest hit for each of these genes are listed in Additional file 2. (B) 439 transcription factor genes regulated during stem development. The two major clusters of genes with similar expression patterns are marked with vertical lines. Gene identities are illustrated in Additional file 5.