Table 1 Ingenuity Pathway Analysis predictions of the effects of supra-physiologic levels of GM-CSF on airway macrophages during IAV. BAL airway macrophages were sorted and RNA-sequencing was performed to compare the gene expression between IAV-infected LM (n = 5 mice) and DTGM (n = 5 mice) treated with doxycycline at 8 dpi. Using the means of each group, the 5% (2181 genes) most expressed transcripts from each of the genotypes, DTGM and LM, were analyzed using Qiagen’s Ingenuity Pathway Analysis (IPA) software. IPA was used to identify differential upstream regulators between AMs (A) and EMs (B) of DTGM and LM mice, and upstream regulators were included in the table if their p-value of overlap was <1E-10 and the activation z-score was < −2 or > +2. IPA was also used to identify differential effects of GM-CSF on canonical pathways of AMs (C) and EMs (D). Ingenuity canonical pathways were included in the table if their -log(p-value) was >10 and the z-score of pathway activation was < −2 or > +2
