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

Identification of transcripts and proteins correlating with the kinetics pattern of the host response to VN1203 wild-type Transcriptomic and proteomic intensity expression matrices of the wild-type VN1203 infected samples have been factorized using a Singular Value Decomposition method. Transcripts and proteins that correlated with at least one eigentranscript or eigenprotein (right-singular vectors) were then identified using the Pearson's coefficient of correlation. We used a cutoff of 0.65 on the Pearson's coefficient of correlation and a cutoff of 0.01 on the p-value associated with this correlation coefficient. The p-values associated with Pearson's coefficients of correlation have been obtained using the Student's t distribution for a transformation of the correlation. 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 identified as differentially expressed at these time-points. In order to discard transcripts or proteins that could contribute to noise the analysis, only the transcripts and proteins found as differentially expressed in at least one biological condition have been used in the SVD analysis.