GRK5 (G protein-coupled receptor kinase 5) was the only annotated down-expressed gene at both 8 hours and 4 days post infection. GRK5 plays a positive role in Crohn’s disease [28]. Salmonella infection increases the risk of inflammatory bowel diseases (IBD) including Crohn’s disease [29]. It is interesting to explore the potential role of AvrA in the

Salmonella-related IBD. Notch3 was annotated with up-regulation at 8 hours post infection, but showed down-expression at 4 days post infection. MS4A7 VX-680 was down-expressed at 8 hours post infection and up-expressed at 4 days post infection. These unique co-regulated genes suggest that AvrA function is differentially regulated in host cells in association with infection time. TGF beta inhibitor Validation of microarray findings with real-time PCR To validate microarray results, we selected 10 differentially expressed genes between SL1344 infection group and SB1117 infection group for qRT-PCR. All of qRT-PCR analyses

were performed in samples previously used for the microarray experiments (Figure 3). Figure 3A and Figure 3B showed the fold times in gene expression in microarray data and real-time PCR measurements at the early stage and the late stage of infection respectively. The gene expression changes measured by qRT-PCR were in agreement with microarray data. Figure 3

Real-time PCR analysis and Microarray Comparison. A: real-time PCR analysis and microarray comparison at the early stage of Infection. B: real-time PCR analysis and microarray comparison at the late stage of infection. The Pearson Aldehyde dehydrogenase correction coefficient between the qRT-PCR and microarray data was 0.836. Therefore, the microarray provided a reliable comparison of gene expression in mouse colon mucous sample from salmonella SL1344 and SB1117 infection at 8 hours and 4 days. Gene Ontology (GO) terms enrichment analysis for genes differentially expressed between the SL1344 and SB1117 infection groups The analysis of enriched GO terms could aid in interpreting the dominant functions controlled by differentially expressed genes. To further address the potential contribution of AvrA to the S. typhimurium SP-I TTSS-mediated stimulation of transcriptional response in mouse intestine, we evaluated the biological processes for these differentially expressed genes, using the GO term enrichment on-line analysis tool, GOEAST (Gene Ontology Enrichment Analysis Software Toolkit) [21]. Table 1, 2, 3, 4 lists important Gene Ontologies with P-values less than 0.05. Table 1 List of biologic process for the up-expressed genes in SL1344 infection group relative to that of SB1117 infection group at 8 hr GO ID Term No.