Figure 5

MDS Projections of the VN1203 mutants infected transcriptomic profiles over the VN1203-WT Reference Map. (A) Multidimensional Scaling Projection (MDS Projection) of the transcriptomic profiles of the VN1203-PB2627E dosage condition over the VN1203 wild-type Multidimensional Scaling Reference Map (MDS Ref Map). (B) MDS Projection of the transcriptomic profiles of the VN1203-HAavir dosage condition over the VN1203 wild-type MDS Ref Map. (C) MDS Projection of the transcriptomic profiles of the VN1203-PB1F2del dosage conditions over the VN1203 wild-type MDS Ref Map. (D) MDS Projection of the transcriptomic profiles of the VN1203-NS1trunc dosage conditions over the VN1203 wild-type MDS Ref Map. Each dot is the transcriptomic profile of a biological sample plotted in the intensity space of gene expression. Pairwise distances between the dots are proportional to the transcriptomic distances between the samples. MDS Projections allow to project additional ‘omics profiles over a predefined MDS representation (MDS Ref Map). Transcriptomic distances have been calculated based on the signature of 5,660 transcripts that significantly correlate with one eigentranscript. Dots are colored in order to indicate the dosage conditions, and biological conditions are indicated by the convex hull (i.e. the smallest convex set containing the points [30]) of the set of biological replicates and labeled to indicate the time point post-infection. Samples and biological conditions of the H5N1 VN1203 wild-type 10⁴ PFU infection dosage are indicated by gray dots and gray convex hulls. Hence the grey spots that are connected represent the -omics profiles of mice lung infected by the VN1203 wild-type virus at 10⁴ PFU, while the ones not connected represent the -omics profiles for the other infection concentrations. 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.