Fig. 3.

Altered SEV proteome is associated with HIV infection comorbid with cocaine use. A Group comparison scheme used to define the COC–, HIV–, and comorbid effects. B Volcano plot showing up- (red) and down- (blue) regulated proteins in the comorbid group as compared to the healthy group. C PCA plot of the 97 comorbid DPPs. Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. X and Y axis show principal component 1 and principal component 2 that explain 33.5% and 10.1% of the total variance, respectively. Prediction ellipses are such that with probability 0.95, a new observation from the same group will fall inside the ellipse. N = 12 data points. D Hierarchical clustering heatmap of the 97 comorbid DPPs. Rows are centered; unit variance scaling is applied to rows. Both rows and columns are clustered using correlation distance and average linkage. 97 rows, 12 columns. E Protein–protein interaction (PPI) network analysis of the 97 DPPs using Genemania