AUTHOR=Arceo Maria E., Ernst Catherine E., Lunney Joan , Choi IgSeo , Raney Nancy E., Huang Tinghua , Tuggle Christopher , Rowland Raymond , Steibel Juan TITLE=Characterizing differential individual response to porcine reproductive and respiratory syndrome virus infection through statistical and functional analysis of gene expression JOURNAL=Frontiers in Genetics VOLUME=3 YEAR=2013 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2012.00321 DOI=10.3389/fgene.2012.00321 ISSN=1664-8021 ABSTRACT=
We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained from blood at 0, 4, 7, 11, 14, 28, and 42 days post-infection (DPI) was hybridized to the 70-mer 20K Pigoligoarray. We used a blocked reference design for the microarray experiment. This allowed us to account for individual biological variation in gene expression, and to assess baseline effects before infection (0 DPI). Additionally, this design has the flexibility of incorporating future data for differential expression analysis. We focused on evaluating transcripts showing significant interaction of weight gain and serum viral level. We identified 491 significant comparisons [false discovery rate (FDR) = 10%] across all DPI and phenotypic groups. We corroborated the overall trend in direction and level of expression (measured as fold change) at 4 DPI using qPCR (