PMC

Representative gel figure showing internal standard. Spots chosen for identification are marked in circles and numbers. The isoelectric point range is 3–10 nonlinear, as indicated on top of the figure. Statistically significant protein spots are color coded red, blue, and green according to .

Western blot validation of differentially expressed protein LDH. Eight patients with TAV, four with dilated and four with nondilated aorta tissues, were chosen for Western blot validation. A, Western blot gel showing LDH and the internal standard TF. B, Box-plot of TF normalized LDH expression (y axis) in four dilated and four nondilated aorta tissue samples from (A).

PCA (A, B) and OPLS-DA (C, D) of protein spot expression data. The analyses were performed on 44 patients and 302 protein spots. The Hotelling's T2 (based on 95% confidence level) tolerance ellipsoid and ellipse are shown in the scores plots of PCA and OPLS-DA, respectively. Three-dimensional scores plot showing the PC1-PC3 plane of nondilated (black) and dilated (red) thoracic aorta tissue samples with TAV (A) and BAV (B) patients separately. Two-dimensional scores plot of an OPLS-DA showing the first predictive component (tp1) and orthogal component (to1) plane of nondilated (black) and dilated (red) thoracic aorta tissue samples with TAV (C) and BAV (D) separately.

Venn diagram and OPLS-DA of protein spot expression data. The significantly differentially expressed protein spots have been calculated with OPLS-DA where ABS (loadings)—ABS (jack-knife confidence interval) if positive indicates significance. The model has been applied on 302 protein spots of dilated versus nondilated samples (44 patients with and without TAA) in TAV and BAV separately. The bar plot of loadings and jack-knife confidence intervals contributing to the first PC for significant spots common for TAV and BAV models, red bars (A), statistically significant only in TAV, blue bars, and BAV, green bars (B) and (C) respectively. D, Venn diagram based on ABS (loading)—ABS (jack-knife confidence interval) significant protein spots of dilated versus nondilated samples in TAV and BAV patients separately (derived from Supplemental Table 2), color coded according to (A)–(C). E, Combined model scatter plot where loadings from TAV model of dilated versus nondilated aorta samples is plotted against loadings from BAV model of dilated versus nondilated aorta samples, color coded according to (A)–(C). Proteins that are significantly differentially expressed only in TAV and BAV are marked in blue and green respectively, whereas proteins that show statistically significant differential expression in both TAV and BAV are marked in red. 109 protein spots chosen for identification by MALDI-TOF are marked with numbers in the combined model scatter plot. The black diagonal is aimed for the interpretation purposes.