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

Multidimensional Scaling representations have been generated using the SVD-MDS method [29] . Multidimensional scaling methods represent the similarities and differences amongst high dimensionality objects into a space having a low number of dimensions, usually in 2 or 3 dimensions for visualization purposes [28] . Pairwise distances between the dots are proportional to the transcriptomic or proteomic distances between the samples. The Kruskal Stress criterion [28] shown in the representations, quantifies the quality of the representations as a fraction of the information lost during the dimensionality reduction procedure. The SVD-MDS method performs the dimensional reduction procedure by using a molecular dynamics approach and by initialing the metric space using a singular value decomposition method, resulting in better representation of the similarities and differences in term of information conservation.