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

To better characterize the host responses, and to be able to quantify their kinetics, we used a Singular Value Decomposition analysis to capture and cluster transcripts and proteins associated with the system's dynamics, as described in [24] . Transcripts and proteins previously identified as differentially expressed in at least one biological condition that correlated with the eigentranscripts or eigenproteins (right-singular vectors of the singular value decomposition) were identified using the Pearson's coefficient, with eigentranscripts or eigenproteins representing significant patterns of expression profiles, associated with the kinetics of the system. Transcripts and proteins that did not correlate with any eigentranscript or eigenprotein, respectively, were not considered as significantly associated in the dynamics of the host response (Pearson's coefficient cutoff = 0.65). This approach was used to examine the host response to VN1203-WT, independently of the inoculation dosage, that was then subsequently used as a reference to compare the VN1203 mutants and CA04-WT. Mock infected biological conditions were not used in the inference of eigentranscripts and eigenproteins, and biological conditions at 1 dpi and 2 dpi were not used in the inference of the eigenproteins because of the relatively low levels of proteins detected as differentially expressed at these time-points.