Figure 2.

Volcano plot of differentially expressed proteins in mutant vs. control mouse. ANOVA analysis was performed on the log₂ transformed peptide intensity data from replicate optic nerve preparations for WT (n=4) and the Phr1-rko mutant (n=4) using the DAnTE-R software. The aligned intensities for the qualified peptides are given in Table S3. The protein level ANOVA comparisons were performed after using the peptide ‘R-Rollup’ utility in DAnTE-R. Only the proteins that contained a minimum of two unique peptide sequences were quantified using the R-Rollup option and these are listed in Table S4. Proteins with significantly different expression are shown above the thick line. The circle on the left encompasses the proteins (n=10) with significant down regulation in the Phr1-rko mutant compared to WT. Those within the circle on the right (n=20) are proteins that were significantly increased in the mutant versus control mice, including the protein hnRNP-M. The results of the ANOVA including significantly and not significantly changed proteins are given in Table S4.