Figure 3. Sox11 overexpression induces changes in transcripts with roles in cell stress, axon growth, and other functions.

(A) Overview of RNA-sequencing and analysis.

(B) Partial listing of Gene Ontology (GO) Biological Process terms. GO terms were generated separately for genes up-regulated or down-regulated (thresholded at FDR < 0.05) by AAV-Sox11 relative to AAV-PLAP. After Bonferroni correction, 57 terms were significantly enriched in up-regulated transcripts, and 144 in down-regulated transcripts. This panel shows the 20 GO terms with the largest sum of Fold Enrichment from up- and down-lists, then sorts the terms by direction of enrichment. Numbers in black indicate the overall number of genes in the GO term definition; numbers in blue and red indicate the number of differentially expressed genes at FDR < 0.05 that are listed in the given GO term definition. Bars indicate the Fold Enrichment over the number of genes expected to appear if genes were randomly selected. Asterisks indicate significance of GO term enrichment: *, p < 0.05; **, p < 0.01; ***, p < 0.001. The full list of significant GO terms is provided in Supplemental Table S2, alongside the enrichment scores and p-values.

(C) Heatmap showing a selection of differentially expressed genes between AAV-PLAP and AAV-Sox11 after crush. The 15 most significant genes (by smallest FDR value) are given for genes that are either up-regulated (red) or down-regulated (blue) by AAV-Sox11 relative to control. Color values indicate log2 transforms of expression values as specified in the color key (bottom), where all values are relative to the average expression in the AAV-PLAP Crush group. The columns correspond to individual samples, with each treatment group performed in triplicate.

(D) Retinal sections were immunostained for Doublecortin/DCX in either intact or post-crush samples as indicated. Scale bar: 50 µm.