Figure 5 of Brooks, Mol Vis 2011; 17:3034-3054.

Figure 5. Heatmaps and hierarchical clusters of differentially expressed rod-specific genes and cone-specific genes or those involved in retinal remodeling. Heatmaps with dendrograms of clusters of differentially expressed rod genes (A) and cone / retinal remodeling genes (B) by applying hierarchical clustering. A filtered list of mRNA transcript isoforms was further revised for fold change ≥1.5 and p-value <0.05, and duplicate gene symbol rows were deleted to retain the most expressed isoform as reflective of the gene. This list was used to generate the heatmap and the master cluster. Specific clusters of rod specific genes and cone-specific or retinal remodeling genes were identified as clusters containing known rod genes (e.g., Rhodopsin [Rho], guanine nucleotide binding protein, alpha transducing 1 [Gnat1], cyclic nucleotide gated channel alpha 1 [Cnga1], and nuclear receptor subfamily 2, group E, member 3 [Nr2e3]) and cone genes (e.g., fatty acid binding protein 7, brain [Fabp7], cyclic nucleotide gated channel alpha 3 [Cnga3], cyclic nucleotide gated channel beta 3 [Cngb3]). Columns 1, 2, and 3 are wild-type samples, and columns 4, 5, and 6 are Nrl−/− samples.