Figure 3

Expression profiles in the fovea. (a) A schematic depicting the areas where the punches were collected for RNA-seq analysis. The punch size was 1.5 mm in diameter. A fovea is marked by an asterisk. c, central; p, pecten; n, nasal; t, temporal. (b) The differences in gene expression profiles in between the fovea and the periphery are displayed in a MA plot (upper panel) and a volcano plot (lower panel). In the MA plot, M is log2 (FC), and A is log2 (average RPKM). In the volcano plot, X-axis denotes log2 (FC) and Y-axis denotes − log10 (adjusted p-value). Red color indicates genes with significant adjusted p-values (< 0.05). (c) A heat map of the genes with significant alterations in expression between the central and peripheral retina for the up-regulated and down-regulated genes (right and left panels). The peripheral retina contains both nasal and temporal retinal regions. Gene expression values were z-transformed for visualization using color scale from blue to red. (d) The top 10 most significantly enriched biological processes determined by gene ontology enrichment analysis for up-regulated and down-regulated genes (upper and lower panels). X-axis is − log10 (adjusted p-value) and Y-axis is biological processes.