Figure 1
Hierarchical Optimal k-Means clustering (HOkM) reveals a splitting into two clusters of the gene expression in the ICM of the mouse embryo at E3.25. (A) Bi-dimensional Principal Component Analysis (PCA) of transcriptomics data from all in vivo wild type samples (Table 1). Dodecahedra and spheres mark bulk and single cells, respectively. Green, cyan and magenta dodecahedra mark bulk samples of oocytes, E1.5 and E2.5-E3.0 cells, respectively. Green, cyan and dark blue spheres mark the E3.25, EPI (E3.5 and E4.5) and PE (E3.5 and E4.5) cells of Ohnishi et al.3, respectively; while the red spheres mark the E3.5 ICM cells of Kurimoto et al.9, and the magenta spheres mark the Prestreak and Early/mid bud cells of Kurimoto et al.56. The arrows infer the direction of development. (B) Bi-dimensional PCA of the single cell transcriptomics data from E3.25 and E3.5 of Ohnishi et al.3. The green spheres mark the E3.25 cells, while the cyan and dark blue spheres mark the E3.5 EPI and E.3.5 PE cells, respectively. The two green ellipses encircle the two groups of E.25 cells, posteriorly classified by the HOkM method and named as E3.25-LNCs and E3.25-HNCs. (C) Violin plot of the silhouettes of the HOkM trajectories. The green line marks the position of the medium silhouette distributions. (D) Dendrogram of the optimal clustering (ko = 2).
