Yamamoto et al. BMC Genomics 2012, 13:335 http://www.biomedcentral.com/1471-2164/13/335 Table 1 Top 25 GO categories overrepresented in LI of 0WexGF mice compared with GF mice Term ribosome biogenesis and assembly antigen processing and presentation of exogenous peptide antigen via MHC class II Number of Probes Page 5 of 15 p_int < 1.0E-18 6.18E-08 1.16E-07 6.79E-07 1.09E-06 1.61E-06 2.00E-06 2.63E-06 2.68E-06 3.64E-06 5.07E-06 6.65E-06 1.32E-05 1.52E-05 1.54E-05 2.46E-05 2.84E-05 3.24E-05 3.92E-05 4.33E-05 5.19E-05 5.69E-05 6.54E-05 7.88E-05 8.14E-05 rhythmic process inflammatory response regulation of cholesterol absorption ribosomal protein import into nucleus lipoprotein metabolic process regulation of cell growth cell surface receptor linked signal transduction positive regulation of phagocytosis cardiac muscle contraction central nervous system development axonal fasciculation phagocytosis, engulfment DNA recombination response to stress MAPKKK cascade respiratory gaseous exchange calcium ion transport glucose homeostasis translational elongation midbrain development positive regulation of T cell differentiation integrin-mediated signaling pathway antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 92 14 19 48 5 10 8 64 50 10 11 17 8 7 27 6 30 21 12 44 18 14 8 6 36 GOID GO:0042254 GO:0019886 GO:0048511 GO:0006954 GO:0030300 GO:0006610 GO:0042157 GO:0001558 GO:0007166 GO:0050766 GO:0060048 GO:0007417 GO:0007413 GO:0006911 GO:0006310 GO:0002504 GO:0006950 GO:0000165 GO:0007585 GO:0006816 GO:0042593 GO:0006414 GO:0030901 GO:0045582 GO:0007229 MGP analysis was performed on GO BP categories which contains 4 ~ 99 genes (“Number of Probes”). The categories were sorted according to the integrated p value (p_int) and the top 25 are represented. The categories related to antigen presentation are noted (e.g., “antigen processing and presentation of exogenous peptide antigen via MHC class II”, “inflammatory response”, “positive regulation of phagocytosis”, “phagocytosis, engulfment”, “antigen processing and presentation of peptide or polysaccharide antigen via MHC class II” and “positive regulation of T cell differentiation”). introduction at different times) influenced various TLR- related genes in diverse ways. The most prominent and specific changes were seen in TLR7/9 (enteric micro- biota, irrespective of colonization protocols, strongly decreased TLR7/9 expression) and IRF3 (expression was very low in SPF and 0WexGF mice and high in GF and 5WexGF mice). Discussion In our previous study [36], using GF and SPF IQI mice and the old version of Affimetrix GeneChip (MG- U74Av2), we compared gene expression profiles of LI in GF and SPF mice. A list of genes most affected by the presence of enteric microbiota was generated by the simple Welch's t-statistic and enumeration in the order corresponding to the fold-change. The list clearly indi- cated that the expression of genes related to the induc- tion and production of type 1 IFN, such as Irf3, Irf7, Isgf3g, Ifit1 and G1p2 (ISG15), was markedly decreased in SPF mice compared with GF mice. In situ hybridization and immunohistochemistry indicated that these IFN-related genes were expressed mainly in lamina proprial CD11b+ cells. In another study [37], using a synthetic IFN inducer and an herbal medicine that enhances IFN production, we demonstrated that the dif- ference in the steady-state expression level of these IFN- related genes was correlated with the difference in the timing of IFN-α release triggered by the inducer. In the present study, we used the same mouse strain but a dif- ferent version of GeneChip (Mouse Expression 430A) and employed a completely different strategy and algo- rithm for bioinformatic analysis. In place of single gene analysis, we have adopted a gene set enrichment analysis with the primary aim of identifying the most affected gene sets in terms of statistical significance. The prede- termined gene sets of categories, cascades and pathways have been furnished from public (GO) and commercial (TRANTHPATH) databases. The results indicated that,