Figure 5
LncRNAs show higher heterogeneity of expression than mRNAs.
(A–E) LncRNAs have higher cell-to-cell variation in expression than mRNAs. Coefficient of variation (CV) across all cells of a given single-cell RNA-seq data set was calculated for each expressed gene (>3 FPKM), and shown are box plots of CV values for highly expressed (>30 FPKM) mRNAs (dark orange) and lncRNAs (dark grey), and for moderately expressed (3–30 FPKM) mRNAs (light orange) and lncRNAs (light grey). Box shows the first and third interquartile range (IQR), the line inside the box shows the median, and whiskers encompass the CV values within 1.5 IQR below and above the first and third quartiles, respectively. Points outside the whiskers are CV outliers. All possible pairwise comparisons result in statistically significant differences, Welch’s t-test (p-value < 0.001). (F–J) Higher fraction of lncRNAs is classified as highly heterogeneously expressed, as compared to mRNAs. Plotted are density distributions of numbers of expressing cells calculated for lncRNAs (black dashed line), mRNAs (red dashed line), lncRNAs and mRNAs together (grey bars), and for modeled populations of genes with high (solid light blue line) or low (solid dark blue line) heterogeneity of expression. Pie charts demonstrate fractions of lncRNAs and mRNAs associated with the population of genes with high (light blue), low (dark blue) or uncertain (grey) heterogeneity of expression. Genes used for this analysis had expression >3 FPKM in at least one cell, and <30 FPKM in all cells of the corresponding data sets. Genes that contributed to the plots and pie charts on (F–J) were classified as belonging to either of the modeled populations of genes (with high or low expression heterogeneity) with a posterior probability >0.99, or were assigned the “uncertain heterogeneity” classification otherwise (posterior probability ≤0.99) (Tables S4,S5,S6,S7,S8). Single-cell RNA-seq data sets re-analyzed here were from: ref. 7 (8-cell and morula stage embryos, hESCs), ref. 53 (K562 cells), and ref. 54 (7W hPGCs and 19 W hPGCs). Number of individual cells used for each analysis is in parentheses in each panel heading.
