Figure 2

Results of proteomics analysis and quality control measurements. (A) Venn diagram indicating the overlap between the proteins identified and quantified from vitreous and retinal tissues (1% FDR). (B,C) Volcano plots demonstrating the dual thresholds for differentially regulated proteins. Each data point represents a single quantified protein. The x-axis represents log fold change in abundance (glaucoma/control). Vertical blue lines indicate 1.3 and 0.77 ratio. The −log (p-value) is plotted on the y-axis. Proteins above the red horizontal line indicate significance ≤ 0.05. Proteins within the upper and outer quadrants meet both the fold change and p-value cut-off, and are therefore considered as differentially regulated. (D,E) Heatmaps (hierarchical clustering) of the log-transformed ratios of differentially expressed proteins (glaucoma vs. control) in retina and vitreous. Column colours indicate treatment type. Red and green color-coding indicate relative increase or decrease in protein abundance, respectively. (F) Venn diagram representing the overlap between the differentially regulated proteins quantified in vitreous and retinal tissues (glaucoma vs. control, p-value ≤ 0.05, ≥ 1.3-fold or ≤ 0.77-fold.