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Table 1 Overlap of LAPs with domain boundaries, recombination HSs and DSB-prone regions

From: Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline

a) Feature Feature count Genomic span (Mb)   
LAPs 14,737 73.69   
Boundaries 40,615 250.89   
HSs 32,984 181.79   
DSB-prone regions 84,946 34.69   
b) Intersection Number of LAPs Fraction of LAPs Expected fraction (circular permutations) p value
LAPs ∩ Boundaries 6960 0.47 0.15 < 10−4
LAPs ∩ HSs 2385 0.16 0.12 < 10−4
LAPs ∩ DSB-prone regions 10,133 0.69 0.14 < 10−4
c) Intersection Number of LAPs Fraction of LAPs Expected fraction (feature intersection) p value
LAPs ∩ HSs ∩ DSB-prone regions 1709 0.12 0.11 < 0.001
LAPs ∩ HSs ∩ boundaries 1172 0.08 0.08 < 0.05
LAPs ∩ HSs ∩ boundaries ∩ DSB-prone regions 836 0.06 0.05 < 0.05
  1. a The number of features and their genomic span. b The number of LAPs that overlap with domain boundaries, HSs or DSB-prone regions, as well as the fraction of unique LAPs in each intersection (as a proportion of the total dataset of 14,737 LAPs). The expected fraction (column 4) and the corresponding p value (column 5) were calculated based on 10,000 circular permutations in R. c Columns 2 and 3 as in b. The expected fraction (column 4) was calculated by multiplying the respective fractions shown in column 3 of b. For example, the fraction of LAPs in the intersection “LAPs ∩ HSs ∩ DSB-prone regions” is equal to 0.16 × 0.69 = 0.11. The hypergeometric test was used to assess the statistical significance of overlap (column 5)