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Fig. 4 | Genome Biology

Fig. 4

From: CRUP: a comprehensive framework to predict condition-specific regulatory units

Fig. 4

Dynamic enhancer-gene pairs in mouse embryo midbrain. a Dynamic enhancer regions, colored by their respective enhancer probability, for eight time points (day 10.5 to day 0 after birth (AB)) in mouse embryo midbrain. A clustering was performed based on the pairwise p values. Enhancer regions that are active in just one condition are highlighted on the right site of the plot. b Distances between dynamic enhancers and their correlated genes (orange) and the respective nearest genes (blue) show the strong discrepancy between the two strategies to find putative enhancer targets. c Schematic description of possible relationships between (1 or many) enhancers and (1 or many) target promoters. d Enhancer probability tracks of the eight time points are summarized on top. Seven differential enhancers could be assigned across all conditions (blue-shaded rectangles). Of these, enhancer probabilities of three regions (dotted blue arcs) highly correlate (correlation coefficient ≥0.9) with the gene expression of Sall4 (bold, gray arrows), a gene that regulates early embryonic development. CaptureC-seq data (CC) of mouse embryo midbrain at day 10.5 (yellow histogram) visually recapitulate these regulatory units. Two of three interaction peaks agree with our dynamic regulatory unit regions (yellow arrows). Additionally, one regulatory unit could be identified solely with CRUP (blue arrow)

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