HIV susceptibility and resistance gene expression. (A) Monocytes, DCs, and macrophages were prepared and RNA was extracted and processed for microarray analysis using the Affymetrix system. Relative transformed expression intensity values were calculated within probe set (row) and hierarchically clustered (“Materials and methods, Oligonucleotide microarray data processing and analysis”), and the corresponding heat map and dendrogram are shown here (red indicates above-average expression; black, average expression; and green, below-average expression for genes associated with HIV resistance and susceptibility). Some genes were represented by multiple probe sets that often fall within the same cluster. Those that show distinct expression behavior may suggest the presence of splice variants (eg, Dicer 1 in clusters 2 and 4). (B) Using the clusters from panel A, parallel line plots by cluster-compare gene-expression profiles in monocytes, DCs, and macrophages from 3 donors. (C) Monocytes, DCs, and macrophages were unstimulated or treated with LPS for 1 hour and RNA was extracted and processed for microarray analysis using the Affymetrix system. Data were treated as in panel A. Data shown are for all 11 probe sets corresponding to the APOBEC cytidine deaminase gene superfamily, represented on the U133Plus2 chip. (D) Parallel line plot comparing APOBEC3 family gene-expression profiles in monocytes, DCs, and macrophages from 3 donors for the 6 probe sets having more than 50% present calls (206632_s_at - 3B, 204205_at - 3G, 209584_x_at - 3C, 210873_x_at - 3A, 214995_s_at - 3G/ 3F, 214994_at - 3F).