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Table 2 Enrichment of protein binding and open chromatin signal in the vicinity of SM breakpoints

From: Functional chromatin features are associated with structural mutations in cancer

  ChIP-seq log2OR DnaseI log2OR Faire log2OR
SM callset Neara Farb Δc    Δc    Δc
    (far-near) Neara Farb (far-near) Neara Farb (far-near)
Breast-Menghi 0.36 ± 0.14 0.93 ± 0.71 0.58 ± 0.69 0.27 ± 0.06 0.89 ± 0.12 0.61 ± 0.11 0.24 ± 0.23 0.89 ± 0.38 0.65 ± 0.24
p = 7.7E-172 p = 6.1E-89 p = 1.5E-47 p = 1.9E-84 p = 1.5E-109 p = 1.4E-91 p = 2.3E-04 p = 8.1E-09 p = 7.7E-10
n = 397 n = 397 n = 397 n = 122 n = 12 n = 122 n = 19 n = 19 n = 19
Colorectal-Bass 0.10 ± 0.16 1.06 ± 0.95 0.95 ± 0.96 0.03 ± 0.06 0.96 ± 0.21 0.93 ± 0.22 0.01 ± 0.32 1.15 ± 0.40 1.14 ± 0.46
p = 2.0E-28 p = 3.5E-62 p = 4.9E-53 p = 7.5E-06 p = 1.5E-82 p = 1.5E-78 p = 9.3E-01 p = 3.1E-10 p = 2.3E-09
n = 345 n = 345 n = 345 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
HeadNeck-Stransky -0.41 ± 0.29 1.24 ± 1.35 1.65 ± 1.43 -0.27 ± 0.10 0.36 ± 0.49 0.63 ± 0.50 -0.25 ± 0.28 0.21 ± 0.87 0.46 ± 0.77
p = 1.2E-52 p = 7.0E-31 p = 8.3E-42 p = 1.5E-58 p = 5.9E-13 p = 8.6E-27 p = 1.1E-03 p = 3.1E-01 p = 2.0E-02
n = 217 n = 217 n = 217 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
ETSwt/CHD1del subset of Prostate-Baca -0.85 ± 0.31 0.05 ± 0.69 0.90 ± 0.63 -0.71 ± 0.21 0.16 ± 0.28 0.86 ± 0.16 -0.40 ± 0.46 0.39 ± 0.45 0.78 ± 0.24
p = 3.6E-189 p = 1.5E-01 p = 3.4E-98 p = 2.1E-67 p = 6.8E-09 p = 4.1E-92 p = 1.3E-03 p = 1.5E-03 p = 3.6E-11
n = 400 n = 400 n = 400 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
ETS+/CHD1wt subset of Prostate-Baca 0.37 ± 0.14 0.92 ± 0.70 0.55 ± 0.71 0.28 ± 0.04 0.93 ± 0.17 0.65 ± 0.16 0.21 ± 0.15 0.87 ± 0.40 0.66 ± 0.32
p = 2.1E-158 p = 5.4E-78 p = 2.3E-37 p = 8.0E-102 p = 1.0E-92 p = 1.4E-78 p = 1.5E-05 p = 2.1E-08 p = 3.9E-08
n = 348 n = 348 n = 348 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
Ovarian-McBride 0.40 ± 0.19 1.32 ± 0.80 0.92 ± 0.80 0.30 ± 0.07 1.05 ± 0.29 0.75 ± 0.25 0.18 ± 0.23 0.99 ± 0.22 0.80 ± 0.17
p = 1.0E-130 p = 9.3E-102 p = 2.6E-66 p = 1.8E-81 p = 8.2E-71 p = 1.1E-62 p = 2.9E-03 p = 1.1E-13 p = 7.5E-14
n = 352 n = 352 n = 352 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
Breast-NikZainal 0.17 ± 0.12 1.24 ± 0.94 1.07 ± 0.96 0.16 ± 0.05 1.16 ± 0.15 1.00 ± 0.16 0.12 ± 0.18 1.15 ± 0.47 1.03 ± 0.36
p = 3.2E-93 p = 1.2E-82 p = 1.4E-66 p = 1.5E-69 p = 1.5E-108 p = 4.9E-98 p = 8.6E-03 p = 2.9E-09 p = 2.1E-10
n = 368 n = 368 n = 368 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
Prostate-Berger -0.27 ± 0.19 0.45 ± 0.77 0.72 ± 0.77 -0.26 ± 0.16 0.39 ± 0.25 0.65 ± 0.16 -0.10 ± 0.35 0.54 ± 0.33 0.64 ± 0.32
p = 1.7E-82 p = 1.4E-22 p = 1.7E-47 p = 1.4E-35 p = 3.8E-34 p = 2.2E-76 p = 2.2E-01 p = 1.3E-06 p = 7.4E-08
n = 332 n = 332 n = 332 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
Prostate-Baca -0.11 ± 0.12 0.37 ± 0.65 0.48 ± 0.62 -0.16 ± 0.08 0.44 ± 0.24 0.60 ± 0.18 -0.07 ± 0.23 0.58 ± 0.40 0.64 ± 0.24
p = 1.4E-60 p = 2.3E-27 p = 9.7E-45 p = 9.5E-43 p = 3.6E-41 p = 1.0E-68 p = 2.3E-01 p = 6.8E-06 p = 8.5E-10
n = 413 n = 413 n = 413 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
Breast-Stephens 0.40 ± 0.12 1.28 ± 0.68 0.88 ± 0.68 0.34 ± 0.04 1.21 ± 0.15 0.88 ± 0.13 0.27 ± 0.22 1.27 ± 0.36 1.00 ± 0.22
p = 5.6E-210 p = 3.0E-130 p = 3.1E-85 p = 5.4E-112 p = 8.6E-112 p = 1.9E-102 p = 5.0E-05 p = 1.0E-11 p = 1.5E-13
  n = 389 n = 389 n = 389 n = 122 n = 122 n = 122 n = 19 n = 19 n = 19
  1. Enrichment of protein ChIP-seq and two open chromatin assays (DNaseI and FAIRE) signal in all SM callsets. Data in each cell show log2 odds ratio (mean ± standard deviation; positive values indicate enrichment). In each table row, only those protein ChIP-seq and open chromatin experiments, that have a non-zero entry in each cell of the 2 × 2 × 2 contingency table, were used; the number of such experiments is shown as n. Δ indicates difference of log OR between the regions near and far from genes.
  2. ap-value calculated against a null hypothesis of log OR being 0 near genes.
  3. bp-value calculated against a null hypothesis of log OR being 0 far from genes.
  4. cp-value calculated against a null hypothesis of no difference in odds ratio between near and far from genes.