Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Tchitchek, Nicolas; Eisfeld, Amie J; Tisoncik-Go, Jennifer; Josset, Laurence; Gralinski, Lisa E; Bécavin, Christophe; Tilton, Susan C; Webb-Robertson, Bobbie-Jo; Ferris, Martin T; Totura, Allison L; Li, Chengjun; Neumann, Gabriele; Metz, Thomas O; Smith, Richard D; Waters, Katrina M; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G

Importantly, these kinetic properties of the host response may not be fully captured by traditional statistical methods that largely depend on different assumptions and applied criteria. For instance, methods used for the identification of differentially expressed genes and over-represented pathways can be negatively impacted by 1) gene magnitude changes, via the fold-change cutoff, 2) the dynamics of the host responses, as biological condition comparisons are usually performed within a given time-point, and 3) the variability of the biological conditions, via the p-value cutoff. For example, the comparison of the VN1203 wild-type condition at 10 4 PFU and at 2 dpi with the VN1203-PB1F2del condition at 10 3 PFU and at 2 dpi will detect a large number of differentially expressed transcripts or proteins ( Figure 5C ). On the other hand, a comparison of the VN1203 wide-type condition at 10 4 PFU and at 2 dpi with the VN1203-PB1F2del condition at 10 3 PFU and at 2 dpi will detect a smaller number of differentially expressed transcripts and proteins. However, in both cases, the virus triggered the same host response mechanisms, but with different kinetics.