Yin et al. BMC Genomics 2010, 11:612 http://www.biomedcentral.com/1471-2164/11/612 Page 3 of 18 Figure 1 Effects of E. purpurea tissue extract [BF/S+L/Ep] on expression of cell-surface markers in mouse bone marrow-derived immature dendritic cells. DCs were examined for the expression of CD40, CD80, CD86, MHC class II and CD11c following [BF/S+L/Ep] for 24 hr by flow-cytometry. level in two independent experiments were considered for further analysis. Differences in expression level were calculated by dividing the signal intensity values of genes from [BF/S+L/Ep]-treated cells by the intensity values of genes from the vehicle-treated (control) cells. Overall, similar numbers of genes were up-regulated and down-regulated after treatment with [BF/S+L/Ep] (Table 1). The expression of 29 genes more than doubled in [BF/S+L/Ep]-treated DCs, compared to vehi- cle control, at 4 h post-treatment, and a group of 31 genes were up-regulated (i.e., ≥ 2-fold change) at 12 h post-treatment. In contrast, 26 and 35 genes were down-regulated (expression more than halved) in [BF/ S+L/Ep]-treated DCs at 4 h and 12 h post-treatment, respectively (Table 1). It is important to note that two different sets of 51 non-immune related genes were highly affected at 4 h and 12 h time points (Table 1). The relative changes in gene expression levels in [BF/ S+L/Ep]-treated DCs are shown in Table 2 and Table 3 for 4 h and 12 h treatments, respectively. The unknown genes and sequences are not shown in these tables. A number of genes that are reported to be differentially expressed in defined immune responses were found to have increased expression after treatment with [BF/ S+L/Ep] [10]. These genes include angiomotin (Amot), chemokine (C-X-C motif) ligand 5 (Cxcl5), pro-platelet basic protein (Cxcl7) and immunoresponsive gene 1 (Irg1) which were up-regulated at 4 h post-treatment with [BF/S+L/Ep], and other genes including cytotoxic T- lymphocyte-associated protein 4 (Ctla4) and chemokine (C-X-C motif) ligand 7 (Cxcl7) were strongly up-regulated at 12 h post-treatment. Among them, Cxcl7 was up- regulated at both 4 h and 12 h time points (Table 2 and 3). In addition, the expression of DC surface marker genes, such as Cd40, Cd80, Cd86, Mhc II and Cd11c, showed little or no changes after [BF/S+L/Ep] treatment, confirming our previous flow cytometric analysis (Figure 1). A number of the responsive genes found here have not previously been shown to be differentially expressed in DCs. Some of these include specific cell surface mole- cules related to cell adhesion or to regulation of cytoske- leton molecules, such as cadherin 10 (Cdh10), cadherin 1 (Cdh1), integrin a6 (Itga6), neural cell adhesion molecule 2 (Ncam2), microtubule-associated protein 9 (Mtap9), Cd38, and gap junction protein alpha 1 (Gja1). RNA transcript levels for genes encoding several secreted