Fig. 1
From: Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
High uncertainty of marker gene expression in single cells and the workflow of reCAT. a Violin plots of distributions of normalized relative expression levels of cell cycle genes, including Ccne1, Pcna, Cdc6 and Hjurp, at three stages (G1, S, G2M) using 232 mESCs. b A 3 × 3 drop density plot for comparison of two groups of cells based on the number of cell cycle-related genes with maximum mean expression at each of the three cell cycle stages. At the two top panels, a set of 60 high-confidence cell cycle related genes (Supplementary Table 1), with a comparable number from each cell cycle stage at which they are known to have maximum expression levels, were used for comparisons. The size of each disk in the matrix is proportional to the number of genes in the entry. The hESC cell group consists of 228 human embryonic stem cells labeled by FUCCI30, and the mESC-Quartz consists of 21 single mESCs labeled by Hoechst staining for cell cycle stages and sequenced by Quartz-seq23. The two bottom panels show comparisons among three cell lines, including H9, MB and PC3 from a data set marked as 3Line-qPCR, and mESC-SMARTer. Cells in 3Line-qPCR were labeled by Hoechst staining, and expression levels of 110 cell cycle related genes were measured by qPCR24. All 110 cell cycle-related genes were used for the comparisons. Pearson’s correlation coefficient (ρ) was calculated for each pair of groups. c The overview of reCAT
