Fig. 4

Transcription factor motif analysis at genes being misregulated in the heart of WRF rats. A Genomic location of DNase I hypersensitive sites in the rat heart (average signal of two independent DNase-Seq datasets). B Overlap between rat and mouse DNase-Seq peaks in the heart. Rat heart DNase-Seq peaks were converted to mouse 10mm genome with LiftOver and then overlapped with mouse heart DNase-Seq peaks (ENCODE project dataset). 76% of the lifted-over rat DHS overlapped with the mouse ENCODE dataset. C IGV browser visualization of rat and mouse DNase-Seq reads at two syntenic genomic regions to illustrate the conservation of DNAse-Seq peaks between the two species. D Motif analysis at DNase I hypersensitive sites located within genes being downregulated or upregulated in WRF rats. Motifs with a q value < 0.05 are colored from yellow to red with red being the most significant. Lack of enrichment for a motif (p > 0.05) is displayed in gray. Diameter of each circle is also proportional to the enrichment q value, with higher diameter for lower q values. Transcription factors expressed in the rat heart are illustrated with a checkmark and those that are not expressed in the rat heart are labeled ne. E Expression profiles of several transcription factors whose motif is enriched in DNase-Seq peaks located in genes upregulated in WRF rats. Each dot represents individual fpkm values. Groups with different letters are significantly different (p < 0.05, Kruskal–Wallis test)