Yamamoto et al. BMC Genomics 2012, 13:335 http://www.biomedcentral.com/1471-2164/13/335 Page 8 of 15 Figure 7 Signal pathways overrepresented in LI of 0WexGF, 5WexGF and SPF mice compared to GF mice. MGP analysis was performed using signal pathways and chains in the TRANTHPATH database. The pathways/chains were sorted according to the integrated p-value (q) and those with q < 0.001 have been represented. Some pathways/chains were classified by their biological contexts and colored as represented in the figure. together with TLR signaling and Rac1 signaling, the sig- naling cascade for the production of type 1 IFN was most prominently affected in SPF and 0WexGF mice. Further, in good accordance with our previous paper [37], the changes in gene expression profiles were dis- similar between SI and LI of SPF mice, while those in GF mice showed substantial commonality between SI and LI. The gene expression profile of SPF mice was similar to that of 0WexGF, particularly in LI, but not to that of 5WexGF mice. The main differences were observed in TLR, Rac1, and IFN-α signaling. TLRs play an important role in the recognition of microbes by host sentinel cells that contribute to subsequent innate and adaptive im- mune responses [39]. TLRs recognize molecular patterns specific for microbes to eliminate pathogens and engen- der commensal colonization of symbiotic bacteria [40]. Therefore, the difference in TLR signaling may contrib- ute to the altered immune function of 5WexGF mice. Similarly, 5WexGF mice may have unique characteristics with respect to the IFN-α response, which is critically important not only for protection against infection by virus and certain microorganism, but also for control of autoimmune responses. Only in 5WexGF intestines, both SI and LI, large scale alteration of chemokine sig- naling was observed. In response to microbial stimuli, fetal intestinal epithelial cells release chemokines very rapidly, and this response may be a prerequisite for in- testinal tolerance to commensal bacteria [41]. Acute chemokine release in response to microbial activation was subsequently maintained for several days in GF mice, but did not occur in mice harboring conventional microbiota due to tolerance acquisition at birth [42]. To clarify how the observed changes in the expression