Fig. 5

Hierarchical clustering and epigenetic data reveal groups of similarly regulated genes. a Hierarchical clustering analysis of all genes that showed significantly altered expression (FC ≥ 2 or ≤ −2, FDR ≤ 0.05) in at least one mutant genotype relative to age-matched WT expression. Expression levels in the indicated genotypes at the indicated ages are indicated by the blue–red heatmap. Eight groups of genes (indicated by the bars on the right) are clearly defined by the results (see Additional file 11 for designations). b Heatmaps showing the epigenetic landscape near the transcription start site (TSS) of genes in groups 1, 2, 3, and 6. Each row represents ±1 kb from the TSS (at center of panel) of individual genes contained within the groups as noted on the left; rows are ordered within each group by decreasing DNase I hypersensitivity (DHS) at the TSS in the 8-week dataset. Columns 1–2, CRX binding determined by ChIP-seq in adult WT and Nrl−/− retinas, respectively; column 3, NRL ChIP-seq in adult WT retinas; columns 4–6, DHS of WT retinas at three indicated ages; columns 7–8, H3K4me2 ChIP-seq in WT retinas at P1 and P15, columns 9–10, H3K27me3 ChIP-seq in WT retinas at P1 and P15. Quantification is presented in Additional file 13