Figure 3.

CC-lincRNAs Are Associated with Stem Cell Cycle Adaptations

(A–C) (A) Distribution of tissue specificity (measured as Tau) for CC-lincRNAs, CC-PCGs, and annotated cell cycle genes. Distribution of the fold difference in expression of (B) lincRNAs and (C) protein-coding genes during a 216-h neuronal commitment of mESCs. Fold difference in expression is relative to the median fold difference at time = 8 h.

(D) Fold enrichment in binding (bars, x axis) of pluripotency transcription factors (y axis) for CC-PCGs (dark gray) and CC-mRNAs (light gray).

(E) Cell cycle stage-average (G1: orange, S: blue, G2/M: green) of the expression Z scores of CC-PCGs (left panel) and CC-lincRNAs (right panel).

(F) Proportional Euler diagram of the number of lincRNAs (left) and protein-coding genes (right) differentially expressed between G1 and S (orange), G1 and G2M (blue), or S and G2/M (green).

(G) Distribution of the correlations between pairs of pluripotency-associated genes (black) or known pluripotency genes, and differentially expressed (CC, gray) or non-differentially expressed (nonCC, white) protein-coding genes and lincRNAs. Significance (two-tailed Mann-Whitney-Wilcoxon rank-sum test) for the comparison between pluripotency-associated genes and the different gene classes is indicated on top of the boxplot as NS p > 0.05, ∗∗p < 0.01, ∗∗∗p < 0.00.