Fig. 4: CNEP score’s relationship to TF sequence motifs and DHS in mouse.

a The plot shows the difference of the distribution of motif enrichments relative to the distribution for a randomized set of the motifs for the PhastCons High_CNE, CNE, Low_CNE, High_notCNE, notCNE, and Low_notCNE bases. The x-axis is the rank position of the motif among the 1646 motifs. The y-axis is the difference between the log₂ fold enrichment based on the actual motif calls and the median log₂ fold enrichment from three randomized versions at the same rank position (see “Methods” section). Similar plots for other constrained elements can be found in Supplementary Fig. 15 and at other thresholds for defining notCNE high bases in Supplementary Fig. 16. b Scatter plot of individual motif enrichments. The x and y axes corresponds to the log₂ fold enrichments in PhastCons Low_CNE and High_CNE bases, respectively. The blue lines separate the three regions used for the GO-enrichment analysis, ‘High_CNE strongly preferred’, ‘High_CNE moderately preferred’, and ‘Low_CNE preferred’, where at least one of the Low_CNE or the High_CNE log₂ enrichment is ≥0.5 (Supplementary Data 3 and 4). The gray line is the y = x line where both Low_CNE and High_CNE log₂ enrichments are <0.5. Similar plots based on other thresholds of the CNEP score can be found in Supplementary Fig. 17. Selected motifs are labeled. c The distribution of enrichments for DHS from 156 experiments in mouse, where the sites are mapped to human and enrichments are computed relative to enrichments for randomized DHS, for PhastCons High_CNE, CNE, Low_CNE, High_notCNE, notCNE, and Low_notCNE bases (see “Methods” section). Similar plots for other constrained elements can be found in Supplementary Fig. 18. d A bar graph corresponding to the enrichments shown in c for Low_CNE bases. Bars are colored to indicate if the experiment is of whole brain or cerebrum, embryonic day 11.5, or neither. Similar plots for other constrained elements can be found in Supplementary Fig. 19. A full set of enrichment values can be found in Supplementary Data 5. Source data are provided as a Source Data file.