Fig. 6
Gene trajectories during differentiation result in overall depletions in repeats. a Exon (top) and intron (bottom) distributions of the lineage-specific genes in the human blastocyst. b Exon (top-left panel) and intron (bottom-left panel) length biases and heatmap of enrichment and depletion scores (right panel) in up-regulated and down-regulated genes during human organogenesis. c Exon (left) and intron (right) length biases in genes that are up-regulated and down-regulated in differentiated embryoid bodies compared to H1/H9 cells. d, e Length biases in exons (top-left panel) and introns (bottom-left panel), and heatmap of enrichment/depletion scores (right panel) in up-regulated and down-regulated genes during human (d) or mouse (e) development. The genes included in this analysis are found up- or down-regulated in all seven developing tissues from the Cardoso-Moreira et al. study as compared to the blastocyst from Xie et al. Observations are based on comparisons of rank normalized genes (see text). Asterisks and crosses indicate a statistically significant difference from the background distribution (P value < 10−4 for an asterisk; P value < 10−2 for a cross; Kolmogorov-Smirnov test)