Scatterplot analysis of the changes in miRNA expression after transfection of HeLa cells with HIV-1 clone pNL4-3. Pairwise comparison of two mock-transfected HeLa cells (sample 1 vs. sample 2) to each other and to pNL4-3-transfected HeLa cells (sample 3) by scatterplot analysis. Spots associated with individual miRNAs were collected and converted into log2 scale. Each datum point represents one unique probe sequence (based on median values from 4 replicated spots from each hybridization). miRNAs with similar signal intensities from the two samples being compared line up together on a 45° diagonal line (center line). This is most clearly seen in (A), where two mock-transfected HeLa cells samples are compared to each other. In this comparison, most of the dots line up together at the center line supporting that the miRNA expression patterns of the two samples (1 and 2) are highly similar. By contrast, miRNAs with expression levels higher or lower in one sample than the other sample are expected to produce dots that deviate from the center line. The dots are allocated to positions that are above or below than the +2 fold or -2 fold line when the differences are greater than two folds. This was the case when the log2 values of sample 3 (pNL4-3-transfected HeLa cells) was plotted against sample 1 (B) or 2 (C). The miRNAs with reduced expression in sample 3 are allocated to positions below the -2 fold line. The red-circled miRNAs were chosen for real-time PCR validation as shown in figure 5.