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. 2021 Sep 22;10(9):bio058617. doi: 10.1242/bio.058617

Fig. 3.

Fig. 3.

Pseudogenes lead to placement of ‘AME cells in the PSA cluster. (A,C) Histogram of coefficient of variation of expressed genes (genes with FPKM>1 in at least 50% cells of a given lineage) across all cells. Principal component analyses (PCA) of 555 cells with variable expressed genes. Variability is defined by a threshold in CV values. The threshold CV and the number of genes that cross the threshold are indicated above the graph. The percentage in x/y labels represents the % of variance in the data explained by each PC. Read counts calculated as log2(fpkm+1) were used for the PCA. Cells are color-coded by the lineages assigned in Xiang et al. (2020). In C, the genes were filtered to include only protein coding genes, prior to determining variable expressed genes. (B) Contribution of different gene biotypes to the first two principal components. Normalized PC coefficient=cumulative PC coefficient for a biotype/cumulative PC coefficient for all biotypes. Cumulative PC coefficient is calculated as the sum of the absolute PC1 coefficient of all genes in that biotype. The two biotypes that contribute the most are shown. (D) PCA plots in C plotted for a subset of cells corresponding to embryonic day 12 and 14.