Gene Expression & Cell Subsets Figure 3. Scatterplots showing log2-fold changes for monocytes (Mono+) compared with non-monocytes (MonoD) and PBMC at 3 and 24 h. Each point corresponds to a gene and represents its differential expression after stimulation with LPS for 3 or 24 h compared to 0 h. The lines represent the cut-off of 50% fold change. Each of the 9 regions separated by the cut-off lines per graph corresponds to a cell in Table 2. doi:10.1371/journal.pone.0004427.g003 specified, the cell type was more specific, reinforcing the findings of different expression in different cell types. Discussion In this study, we quantified the proportion of LPS-induced differentially expressed monocyte genes that could be measured in PBMC, and determined the extent to which gene expression in the non-monocyte cell fraction diluted or obscured fold changes that could be detected in the cell mixture. The effect of gene expression in the non-monocyte fraction diluting or obscuring the detection of expression of particular genes in PBMC was not insubstantial. More than half of the statistically significant LPS-induced changes in gene expression in monocytes were not detectable in the PBMC sample. However, the genes whose expression were most significantly changed in monocytes in response to LPS were those that could also be detected in PBMC as a whole. In our study, almost all genes (97%) with a greater than four fold change were still detectable (figure 4b). Future studies to quantify in more detail the diluting effect of differential expression in non-target cells on detectable gene expression of an individual cell type within a mixture, could be PLoS ONE | www.plosone.org 5 February 2009 | Volume 4 | Issue 2 | e4427