Figure 2: Overview of the PLS-DA analysis for the SMA vs CN comparison. (A) Plot of R2Y (explained variation) and Q2Y (predicted variation); it shows how the considered parameters change as a function of increasing model complexity. Note that the PLS-DA modelling resulted in one significant component; however, three components were generated to enable the construction of the 3-dimensional score plot. (B) PLS-DA score plot reveals grouping according to class membership: all patients affected by Spinal Muscular Atrophy (SMA, red cones) are positioned in the left part of the space, whereas all control subjects (CN, blue spheres) are found in the right part of the space. (The axes of the plot indicate PLS-DA components 1-3). (C) Identification of the subquadrants, in terms of pI and MW, with the highest VIPvalues. Protein expression changes in the most influential subquadrants, involved in the discrimination of the disease from the healthy group, are plotted as a heatmap. In this heatmap, a red color reflects expression greater in SMA than CN patients, a blue color less in SMA than CN and a light green color reflects a similar expression in the two groups. (D) Validation plot by permutation test. The X-axis denotes the correlation coefficient between original and permuted data response, whereas the Y-axis shows the R2Y (triangles) and Q2Y (squares) values of all models. The two last points in the plot correspond to the values of R2Y and Q2Y for the original model. Two regression line have been fitted, one among the R2Y points and another one among the Q2Y points. The two intercepts can be considered as measures of degrees of overfit and overprediciton.