Classification of Visual Cortex Plasticity Phenotypes following Treatment for Amblyopia

Figure 4

Identifying plasticity features using the principal component analysis. (a) .The percentage of variance captured by each principal component by singular value decomposition (SVD) applied using all of the protein expression data. The first 3 principal components capture 54%, 18%, and 10% of the variance, respectively, totalling >80% and thus representing the significant dimensions. (b). The quality of the representation, cos², for the proteins is plotted for each dimension (small/white: low cos²; large/blue: high cos²). (c). The sum of cos² values for the first 3 dimensions for each protein. (d, e). Biplots of PCA dimensions 1 and & 2 and (f, g). 1 and & 3. These plots show the vector for each protein (d, f) and the data (small dots) plus the average (large dots) for each condition with the best-fitting ellipse (e, g). (h). The basis vectors for dimensions 1-3 showing the amplitude of each protein in the vector. (i). The strength (circle size) and direction (blue-positive, red-negative) of the correlation () between each protein and the PCA dimensions. (j). Correlation between the plasticity features (columns) identified using the basis vectors (see Results) and then PCA dimensions 1-3. Filled cells are significant, Bonferroni- corrected correlations (green = positive, red = negative). For the table of Pearson’s values and significant - values for these associations, see Supplemental Table 4-1.

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