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Fig. 4 | Genome Biology

Fig. 4

From: Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

Fig. 4

Physical characteristics of the probe-gene pairs. a A histogram of probe-gene distances for all pairs with a hypomethylated (green) or hypermethylated (yellow) probe. Shown is the distribution of the distance between linked distal enhancer probes and genes. The X-axis shows distances in bins of 50 kb or 200 kb. The Y-axis shows the proportion of all probe-gene pairs in the category (hyper- or hypomethylated) that fall into each range. These were compared to randomized datasets (gray bars), which were generated by randomly selecting 1,000 probes from the full set of 145,265 distal probes, and randomly pairing each with one of its 20 adjacent genes. We generated 1,000 such datasets to generate 95 % confidence intervals for each bin (+/-1.96* SD). b For each probe in a probe-gene pair, the 20 adjacent genes were ranked by distance, and shown is the proportion of all probes linked to genes of a given rank. For this analysis, probes linked to more than one gene and multiple probes linked to the same gene, were omitted

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