Yin et al. BMC Genomics 2010, 11:612 http://www.biomedcentral.com/1471-2164/11/612 Page 4 of 18 Figure 2 Correlation of biological sample replicates. A, DMSO (control) replicates (Affymetrix ID: 579, 580) after 4 h treatment. Pearson correlation value: 0.99735. B, [BF/S+L/Ep] replicates (Affymetrix ID: 581, 582) after 4 h treatment. Pearson correlation value: 0.99303. C, [DMSO] (control) replicates (Affymetrix ID: 583, 584) after 12 h treatment. Pearson correlation value: 0.99628. D, [BF/S+L/Ep] replicates (Affymetrix ID: 585, 586) after 12 h treatment. Pearson correlation value: 0.99631. Data analysis used Spotfire software. Pearson correlation value and number of unchanged transcripts were calculated using GCOS software. proteins were also increased by treatment with [BF/S+L/ Ep]. These genes include chemokine (C-X-C motif) ligand 2 (Cxcl5), pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) (Cxcl7), acid phosphatase (Acpp), chondroitin sulfate proteoglycan 2 (Cspg2), matrix metal- lopeptidase 8 (Mmp8), and serpin peptidase inhibitor (Serpinb2). In comparison, the expression of transcripts encoding several enzymes fell after treatment with [BF/ S+L/Ep]. These genes included protein kinase C (Prkce), acyl-CoA synthetase (Acss1), ST8 alpha-N-acetyl- neuraminide alpha-2,8-sialyltransferase 6 (St8sia6), and Src-like-adaptor (Sla). Moreover, the expression of mRNAs encoding transcription factors or DNA binding proteins localized in the nuclear compartment, such as ankyrin repeat and SOCS box-containing 2 (Asb2) and inhibitor of kappa light polypeptide gene enhancer in B- cells (Ikbkg), were increased in [BF/S+L/Ep]-treated DCs, and the expressions other transcription regulatory genes, such as synaptonemal complex protein 1 (Sycp1), RNA binding motif protein 14 (Rbm14), HECT domain con- taining 1 (Huwe1) and SRY (sex determining region Y)- box 6 (Sox) were decreased (Table 2 and 3). 3. Putative signaling networks involved in modulatory effect of [BF/S+L/Ep] on iBMDCs Functional genomics experimental approaches were employed in our previous study on the modulatory effect of Echinacea plant extracts on human DCs [9,10]. Using the same defined phytocompound extracts here we ana- lyzed the genome-wide transcriptional response in the context of known functional activities and interrelation- ships among specific protein molecules and/or different cell phenotypes by using Ingenuity Systems, a structured network knowledge-based approach, to provide insight