Figure 2

Visualization analysis of the METABRIC dataset using principal component analysis that gives a general view of sample distribution supported by the selected genes and copy numbers. The samples were projected onto a principal curve (the red line) constructed using the first three principal components. Each sample was annotated based on its corresponding PAM50 label. Green, normal; blue, normal-like; cyan, luminal A; magenta, luminal B; yellow, HER2+; black, basal. The 144 normal breast tissue samples were used as the baseline. They are first connected with normal-like and luminal A samples, gradually transit to luminal B and form a bifurcation structure leading to basal and HER2+. The 3D plot can be viewed interactively in Adobe Acrobat by setting Adobe Acrobat -> Preference -> 3D & Multimedia.