Fig. 2: TE-derived conserved and lineage-specific cCREs in human and mouse.
From: Regulatory transposable elements in the encyclopedia of DNA elements
A Classification of shared and lineage-specific cCREs for human to mouse comparison. For orthologous TE-cCREs, syntenic cCRE in mouse is not required but can be present. B Percentage of cCREs that are shared or lineage-specific for orthologous TE and syntenic non-TE human anchored cCRE regions. Shared cCREs are split into “same” and “different” categories depending on the syntenic human and mouse cCRE types. Grouping by cCRE type is done using the anchored human cCRE. Multinomial tests for goodness of fit (log-likelihood ratio, exact or Monte Carlo simulations with 1,000,000 random trials) were performed to compare TE and non-TE distributions (dELS Monte Carlo p-value = 0; pELS Monte Carlo p-value = 0; PLS exact p-value = 3.922 × 10−26; DNase-H3K4me3 exact p-value = 3.975 × 10−16; CTCF-only exact p-value = 7.233 × 10−28; no multiple test correction). C 100-way vertebrate phastCons score distributions for orthologous TEs and non-orthologous TEs associated with human cCREs. One-sided Wilcoxon rank-sum test p-value < 2.2 × 10−16. D 100-way vertebrate phastCons score distributions for orthologous TEs that have cCRE in both human and mouse vs. human only. One-sided Wilcoxon rank-sum test p-value < 2.2 × 10−16. E Percentage of conserved and novel (lineage-specific) cCREs that are TE-derived, split up by cCRE type. Percentages for human and mouse are shown by red and blue dots, respectively. Bars represent the mean percentage between human and mouse. ***p < 0.001.
