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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.
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BMC Genomics

ISSN: 1471-2164

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