28 days post light does not represent transcriptional recovery to either the 0 h, or naïve control transcriptional baseline. (A) Gene Ontology (GO) was performed on the time-course analyses of all significantly differentially regulated genes (DEGs) (p < 0.002) comparing dark-adapted 0 h controls to 28 dpL retinas and (B) non-dark-adapted naïve controls to 28 dpL retinas. Significant DEGs were run through the “Reduce and Visualize Gene Ontology” (REVIGO) software to remove redundant GO terms based on similarity. Circular Visualization plots were generated using the Circular Gene Ontology terms Visualization (CirGO) algorithm displaying up to 20 of the most represented categories. Inner rings represent the hierarchical summary categories identified by the REVIGO software that contain the subcategories in the outer rings that fall under the umbrella term (not shown). Keys to the right of each graph represent labels for the inner ring categories. (C) Principle component analysis constructed using the top 200 genes differentially regulated as compared to the 0 h baseline, with the addition of the non-dark-adapted naïve control group (“nc” dark red) which clustered distinct from both the dark-adapted 0 h controls and the 28 dpL retinas. (D,E) Volcano plots highlighting the remaining significant DEGs in yellow (p < 0.05) at (D) 28 dpL compared to dark-adapted 0 h controls and (E) 28 dpL compared to naïve controls.
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