Yin et al. BMC Genomics 2010, 11:612 http://www.biomedcentral.com/1471-2164/11/612 Page 5 of 18 Table 1 Changes in gene expression in BMDCs in response to treatment with [BF/S+L/Ep] Expression change relative to DMSO alone Up-regulated genes Down-regulated genes Total number of regulated genes Percentage of all genes (%) At 4 h: Total genes Immune- related Non- immune- related At 12 h: Total Genes Immune- related Non- immune- related Significanta ≥1.5 ≥2b ≥3 ≥4 Significanta ≥1.5 ≥2c ≥3 ≥4 ≥2b-c Significanta ≥1.5 ≥2d ≥3 ≥4 Significanta ≥1.5 ≥2e ≥3 ≥4 ≥2d-e 513 104 19 6 3 89 16 4 2 0 15 605 128 21 6 3 144 27 2 1 1 19 472 94 10 5 2 83 14 0 0 0 10 736 132 18 5 3 120 19 0 0 0 18 985 198 29 11 5 172 30 4 2 0 25 1341 260 39 11 6 264 46 2 1 1 37 2.90 0.58 0.09 0.03 0.01 0.51 0.09 0.01 0.01 0 0.07 3.94 0.76 0.11 0.03 0.02 0.78 0.14 0.01 0 0 0.11 aDifferentially expressed genes that are significant in [BF/S+L/Ep] vs. [DMSO] (control). Values of p ≤ 0.05 are considered to be significant. All relative differences greater than 1.5 are significant. bUp-regulated genes with at least a 2-fold change in the level of RNA transcript expression after 4 h treatment. cUp-regulated immune-related genes with at least a 2-fold change after 4 h treatment. dDown-regulated genes with at least a 2-fold change in the level of RNA transcript expression after 4 h treatment. into the regulation of BMDC activities that are relevant to the body immune system. Figure 3A shows the hypothetical or candidate networks revealed by clustering analysis of representative genes involved in the BMDC response to [BF/S+L/Ep] treatment. Apparent temporal controls for coordination of specific gene expressions were classified into three different functional groups: the immune response related genes (Group 1); adhesion molecules, cytoskeleton and cell movement-related genes (Group 2); and the cell cycle, cell proliferation, and apop- tosis-related genes (Group 3). These responses to treat- ment with [BF/S+L/Ep] extract in iBMDCs may be viewed as an integrated cell-wide response involving cell trafficking, attachment, immunity and apoptosis. To identify possible signal transduction pathways in response to [BF/S+L/Ep] treatment, we analyzed, for both the 4 h and 12 h treatments, the 37 up-regulated genes using TRANSPATH software in the manner pre- viously reported [9,10]. Signal transduction pathways involving the CRBP1, AhR, APC and Cyr61 genes with a ≥ 2-fold change in expression level (Table 2) were pre- dicted. Apparent signaling network and functional geno- mic analyses suggest that treatment of DCs with [BF/ S+L/Ep] may activate the JNK, PP2C-a, AKT, ERK1/2 or MAPKAPK pathways, because expression of their downstream genes were up-regulated (Figure 3B). For those down-regulated genes, the TRANSPATH software was not able to predict a matched upstream pathway.