Viral infection resulted in significant alterations of mRNA levels in 1,347 transcripts at 4 hpi and 2,152 transcripts at 24 hpi; these transcripts mapped to 1,077 (4 hpi) and 1,493 (24 hpi) known genes. Tables 1 and 2 show the top 25 genes that were up-regulated or down-regulated by influenza virus. The complete list of altered genes is listed in Data S1. To identify the cellular functions and pathways affected by the infection, the array data were processed by Ingenuity Pathway Analysis (IPA) using IPA version 8.0 (IngenuityH Systems, Redwood City, CA), which associates differentially regulated genes with known specific biological pathways based on information from published literature (www.ingenuity.com). The results from IPA indicate some functional groups of genes were changed at both time points. These genes are involved in antimicrobial and inflammatory responses, cell death, cancer, infection mechanisms, cellular growth and proliferation, cell-mediated immune responses, and immune cell trafficking. Interferon regulatory factor (IRF) activation and PRR signaling were the most prominent pathways activated by viral infection at both time points. In addition, retinoic acid-induced gene-1 (RIG-I) and interferon (IFN) signaling were dominant at 4 hpi, whereas homeostasis-related pathways such as IL-10 and IL-6 were activated at 24 hpi.