Figure 5From: Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stemsHierarchical clustering analysis of the top 200 most differentially expressed genes selected from pair-wise comparisons. Pair-wise comparisons of gene expression were made between stem tissues (ES, PES) in alfalfa genotypes 708 and 773. The RPKM-normalized expression counts for each gene in each library are represented by intensity of the red color on a 0 to 45 scale. Dark red (scale intensity 45) indicates genes with RPKM-normalized expression counts ≥ 45. See Methods for details. Groups I and III, genes differentially expressed in a tissue-specific manner; Groups II and IV, genes differentially expressed in a genotype-specific manner; and Group V, genes differentially expressed in both a genotype- and tissue-specific manner. A complete list of the genes, RPKM-normalized expression counts, and corresponding MapMan functional categories are provided in Additional file 20.Back to article page