Fig. 3

CTCF site cluster spatial distribution analysis reveals orientation biases in the human genome. Spatial distribution of CTCF binding sites and their motif orientation. a Distribution of distances between adjacent CTCF binding sites along the human genome (orange) and in spatially randomised CTCF binding sites (blue). The p value was computed at the hand of the Mann–Whitney U test for the difference between the two distributions. b Number of CTCF clusters at varying clustering window. Starting with a window of 1 bp yields 61,079 mono-plets and using a 10⁸ bp window yields as many clusters as chromosome arms. Shuffled CTCF sites along the genome (blue) are compared to the real spatial distribution of sites (orange). The red line shows the 25-kb clustering window. c For each set of clusters composed of 2, 3 and 4 binding sites and subsequently stratified by their class, we show the distribution of their size (distance from the most upstream to the most downstream binding site). The brackets show the p values obtained in Bonferroni-corrected t tests. d Schematic representation of the clustering and pattern finding process. Clusters are non-overlapping sets of adjacent CTCF binding sites and can be decomposed in their various sub-patterns. In particular, in this representation, given the indicated clustering window, we find three clusters of CTCF sites. We also show that cluster 3 corresponds to 4 mono-plets, 3 di-plets, 2 tri-plets and 1 tetra-plet. ep values calculated with the Pearson chi-square test (see Fig. 2) as a function of the clustering window size used in panel f. f Overrepresented (red) and underrepresented (blue) occurrences of CTCF patterns as a function of the indicated clustering window sizes. The colour scale represents log10 enrichment values (see the ‘Methods’ section). CTCF orientation patterns are ordered by class, as in Fig. 2