Fig. 3: Gene activity correlates with TSS structural embedding and spanned volume. | Nature Communications

Fig. 3: Gene activity correlates with TSS structural embedding and spanned volume.

From: Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

Fig. 3

Top of the figure indicates expression level (RPKM) for each of the selected loci at each reprogramming stage35. a Dynamic structural embedding of the TSS particle. Each central line and the surrounding shadowed area represent respectively the average and the standard deviation interval of the profile over the 100 TADdyn replicates. b Volume explored by the TSS particle during the various stages of the reprogramming dynamics. The convex-hull values are represented as boxplots (n = 100 values for B and PSC and n = 200 values for the other cell stages) showing: central line, median; box limits, 75th and 25th percentiles; whiskers, 1.5× interquartile range. Outliers are not shown. Connecting lines between distributions indicate they are statistically different (p < 0.0001, two-sided Wilcoxon rank sum test). Exact significant p-values are: Sox2 (pBα-D8 = 3.7e-08, pBα-PSC = 8.1e-06, pD2-D4 = 2.0e-06, pD4-D8 = 5.0e-14, pD4-PSC = 7.8e-10, pD6-D8 = 6.9e-09, pD6-PSC = 3.6e-06); Mmp12 (pB-Bα = 7.4e-08, pB-D2 = 4.0e-15, pB-PSC = 2.6e-07, pBα-D8 = 3.8e-17, pBα-PSC = 7.5e-20, pD2-D4 = 3.3e-08, pD2-D6 = 3.5e-10, pD2-D8 = 5.4e-27, pD2-PSC = 7.4e-26, pD4-D8 = 5.4e-11, pD4-PSC = 4.7e-15, pD6-D8 = 1.8e-07, pD6-PSC = 1.9e-11).

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