discovery rate was 0. 01 and the esti mated absolute log2 fold change was 0. 5 in at least one of the pairwise comparisons, which were declared to be differentially expressed during the course of infection. Pathway analysis of DE genes selleck chemicals llc was performed using the Kyoto Encyclopedia of Genes and Genomes database and the two sided Fishers exact test. Only sig nificant pathway categories that had a P value of 0. 05 and an FDR of 0. 05 were analyzed. The significant sig naling pathways included cell adhesion molecules, T cell receptor signaling pathway, antigen pro cessing and presentation, natural killer cell mediated cytotoxicity, Toll like receptor signaling pathway, and complement and coagulation cascades. Validation of DGE data using qPCR and serum cytokine analysis To validate DE genes identified by Solexa sequencing, eight genes were selected for confirmation using qPCR.

The set included two down regulated genes and hyaluronan and proteoglycan link protein 1 and six up regu lated genes, DEAD box polypeptide 58, ubiquitin specific peptidase 18, chemokine C X C motif ligand 10, cytochrome P450 and CD209 Data were presented as fold changes in gene expression normalized to the hypox anthine phosphoribosyltransferase 1 gene and relative to the C sample. Pearsons correlation coefficient demonstrated that the DGE and qPCR data were highly correlated, genes modulated by H PRRSV had a very high consistency and r values ran ged from 0. 935 to 1. 000 between the two methods. qPCR analysis confirmed the direction of change detected by DGE analysis. TNFa expression was elevated 2.

27 to 6. 29 fold in the sera of H PRRSV infected pigs on days 4 and 7 post infection, respectively, compared with C levels. In H PRRSV infected animals, IFN g expression increased 1. 2 fold by 3 d pi, and 4. 3 fold by 7 d pi. STC and STC GO analysis In order to profile the gene expression time series and search for the most probable set of clusters generating the observed time series, the STC algorithm of gene expression dynamics was used, which took into account the Brefeldin_A dynamic nature of temporal gene expres sion profiles during clustering and identified the num ber of distinct clusters. DE genes exhibited eight types of temporal expression pattern with four significant cluster profiles, which have signifi cantly more genes assigned under the true ordering of time points than the average number assigned to the model profile in the permutation runs.

One striking observation was the relative constancy in gene expression profiles of four significant cluster profiles, particularly EPZ-5676 leukemia profiles 6 and 1. The sustained host response in H PRRSV infected pigs indicated that critical decisions influencing the outcome of infection occur very early after infection. Gene Ontology based on biologi cal process enrichment analyses for sets of DE genes having significant cluster profiles was performed using the two sided Fishers exact test. Significant GO categories that had a P value of 0. 05 were used. Th