Figure 3

Eigengenes in the kinetics of the VN1203-WT response, and MDS representations of the infected samples. (A) and (B) Profiles of the eigentranscripts and eigenproteins identified in dynamic of the host response to H5N1 VN1203 wild-type. Number of transcripts and proteins correlating with each eigentranscript and eigenprotein are indicated. All the individual shape represent the transcriptomic or proteomic profile of a mice lung infected by the VN1203 wild-type virus. Biological samples have been sorted by inoculation concentrations and then by increasing days post-infection. (C) and (D) Multidimensional Scaling representations of the transcriptomic and proteomic profiles of the H5N1 VN1203 wild-type infected samples. Each dot in the representations is the transcriptomic or proteomic profile of a biological sample plotted in the intensity space of expression signals. Pairwise distances between the dots are proportional to the transcriptomic or proteomic distances between the samples. Transcriptomic and proteomic distances have been calculated based on the signature of 5,660 transcripts and 162 proteins that significantly correlate with one eigentranscript or eigenprotein. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull of the set of biological replicates and labeled to indicate the time point post-infection. The Kruskal Stress shown in each representation quantifies the quality of the geometrical representation as a fraction of the information lost during the dimensionality reduction procedure. Schematic projections of the Magnitude and Velocity Coefficients are illustrated at 10⁴ PFU in the transcriptomic MDS representation. The Magnitude Coefficient MC at 2 dpi – quantifying the transcriptomic distance between mocks and 2 dpi samples – is illustrated by a dashed red line, and the Velocity Coefficient (VC) at 4 dpi – measuring the velocity between 4 and 2 dpi samples divided by time – is illustrated by an arrow dashed red line.