Additional file 1.

Cuffdiff output of all significant hits for comparison, using the HP-PRRSV rJXwn06 vs. control and the US PRRSV VR-2332 vs. control datasets, to test for differential expression and regulation amongst the two disease states. Gene annotation (symbol) was carried out using a MySQL database matching to the Ensembl Sscrofa9.56 reference genome currently supported by the Integrative Genomics Viewer (Broad Institute). Location (row.names); gene annotation (symbol); entrez gene name; treatment (sample_1, sample_2); status; abundance in FPKM (value_1, value_2); differential expression (log2_fold_change); test statistic (test_stat); p-value (p_value); false discovery rate (FDR)-adjusted p-value of the uncorrected test statistic (q_value); significance status after Benjamini-Hochberg correction for multiple-testing (significant).

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Miller et al. BMC Veterinary Research 2012 8:208   doi:10.1186/1746-6148-8-208