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Fig. 1

Fig. 1. Gene expression in peripheral blood mononuclear cell samples taken from HIV-infected participants before HAART was used to predict after 48 weeks of HAART: (a) the good (ΔCD4 ≥ 200 cells/μl) vs. poor (ΔCD4 < 200 cells/μl) CD4+ T-cell recovery group or (b) the specific ΔCD4 value for each patient. From: Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T-cell recovery.

(a) When predicting recovery group, classification accuracies achieved using different multivariate classification methods were determined for gene expression classifiers containing different numbers of genes. A full description of classification methods can be found in the BRB-Array Tools manual [26]. Support vector machines (SVMs) were the most robust multivariate classification method in which 40 genes attained 100% classification accuracy. (b) When predicting the specific ΔCD4 value for each HIV-infected patient, the LASSO algorithm was used in a cross-validated approach to identify 22 genes whose expression could predict ΔCD4 values that correlated well with actual ΔCD4 values. Predicted ΔCD4 values were then used to assign participants to the good and poor CD4+ T-cell recovery groups based on the ΔCD4 threshold of 200 cells/μl (dotted lines). This allowed the number of true positives (TP), false positives (FP), true negatives (TN), and false negatives (FN) to be determined. Classification accuracy was calculated as [(TP + TN)/(TP + FP + TN + FN)] × 100 and was equivalent to 79%. R refers to the Pearson's correlation coefficient.

Christopher H. Woelk, et al. AIDS. ;24(2):217-222.

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