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Fig. 4 | BMC Bioinformatics

Fig. 4

From: recoup: flexible and versatile signal visualization from next generation sequencing

Fig. 4

a recoup peak center profiles overlaying the DP (red), ST0 (purple), ST1 (green) and mNKT (blue) average chromatin accessibility profiles in iNKT lineage-specific loci. The gradually reducing average read coverage across the TSS indicates the higher accessible chromatin levels from the early stages of invariant NKT commitment. Average signal on the y-axis denotes the average normalized read coverage around the TSS of mouse genes. b recoup heatmaps depicting the average chromatin accessibility profile of naive DP thymocytes and the differentiation stages of the iNKT lineage. As in a, the gradual reduction of chromatin accessibility is depicted by both the number of genes with accessible chromatin around their TSS as well as the signal strength (red colorbars on the right). With respect to a, the heatmaps show detailed normalized read coverage for each gene instead of averaging. c Signal heatmap profiles of the transcription factors CEBP/α and HNF4/α, coupled with RNA PolII binding and H3K27ac histone mark signals around the peak centers of the TFs, located in promoters in adult mouse livers. k-means clustering of the TF and H3K27ac profiles reveals regions of potential enhancers as well as different groups of binding strength with respect to transcription and TF co-binding

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