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Fig. 3 | BMC Genomics

Fig. 3

From: Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Fig. 3

Df and +  Bl6 D DIRs along chromosome 4. a “Rainbow plot” for the 4E2 region representing the DIRs for the comparison between Df and +129, and between +  Bl6 D and + Bl6 computed with a 20 Kb smoothing factor for the viewpoints surrounding the deletion b. Rainbow plots were used to visualize both short and long-range interaction changes. The arcs represent increased interaction (red) or decreased interaction probabilities (blue), with the strength of signal color coded. For visual clarity we only show signals with strength >10 %, and do not include contacts inside the deletion region for +  Bl6 D in b. Grey arrows annotate positions for viewpoints 1, 2 (upstream of deletion) and 11, 12 (downstream of deletion, towards telomeric end). c Positions of DIRs for all viewpoints 1, 2, 11 and 12 are compared against structural protein binding sites. First track is for Df and +129 comparisons and second track is for +  Bl6 D and + Bl6 comparison. DIRs with increased/decreased contact probabilities compared to WT are plotted in red/blue. Shown in the third and fourth tracks (green bars) are the running average over 20 Kb window for CTCF and Smc1 binding site footprint, respectively. The fifth track displays fold change for Df/+  Bl6 D DE genes, color coded (red, over-expressed in Df/+  Bl6 D MEFs; blue, over-expressed in +129/+Bl6 MEFs)

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