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Table 3 Summary of the ORA

From: A genome-wide DNA methylation signature for SETD1B-related syndrome

Gene ontology: biological processes

 

Description

C

O

E

R

pValue

FDR

GO:0051276

Chromosome organization

1143

165

97.67

1.69

5.59E−12

5.08E−08

GO:0033043

Regulation of organelle organization

1245

175

106.39

1.64

1.16E−11

5.26E−08

GO:0007049

Cell cycle

1739

223

148.60

1.50

1.15E−10

3.48E−07

GO:0006915

Apoptotic process

1911

239

163.30

1.46

2.52E−10

5.74E−07

GO:0010941

Regulation of cell death

1648

210

140.83

1.49

7.83E−10

1.42E−06

GO:0006325

Chromatin organization

741

112

63.32

1.77

1.35E−09

1.90E−06

GO:0033554

Cellular response to stress

1867

231

159.54

1.45

1.47E−09

1.90E−06

GO:0010942

Positive regulation of cell death

660

102

56.40

1.81

2.28E−09

2.60E−06

GO:0010629

Negative regulation of gene expression

1733

216

148.09

1.46

3.00E−09

2.87E−06

GO:0034613

Cellular protein localization

1815

224

155.10

1.44

3.44E−09

2.87E−06

Gene ontology: molecular function

 GO:0003723

RNA binding

1603

203

131.47

1.54

7.52E−11

8.28E−08

 GO:0019904

Protein domain specific binding

684

106

56.10

1.89

8.82E−11

8.28E−08

 GO:0001067

Regulatory region nucleic acid binding

898

129

73.65

1.75

1.39E−10

8.70E−08

 GO:0044212

Transcription regulatory region DNA binding

896

128

73.48

1.74

2.38E−10

1.12E−07

 GO:0043565

Sequence-specific DNA binding

1097

146

89.97

1.62

1.87E−09

7.02E−07

 GO:0003690

Double-stranded DNA binding

915

126

75.04

1.68

3.41E−09

1.07E−06

 GO:0000976

Transcription regulatory region sequence-specific DNA binding

781

111

64.05

1.73

5.41E−09

1.45E−06

 GO:1990837

Sequence-specific double-stranded DNA binding

823

115

67.50

1.70

7.55E−09

1.77E−06

 GO:0000977

RNA polymerase II regulatory region sequence-specific DNA binding

729

103

59.79

1.72

2.69E−08

5.62E−06

 GO:0001012

RNA polymerase II regulatory region DNA binding

735

103

60.28

1.71

4.11E−08

7.72E−06

Human Phenotype Ontology

 HP:0002346

Head tremor

20

10

1.87

5.36

3.48E−06

0.016253

 HP:0011337

Abnormality of mouth size

269

43

25.09

1.71

2.13E−04

0.167774

 HP:0004097

Deviation of finger

320

49

29.85

1.64

2.23E−04

0.167774

 HP:0000311

Round face

73

17

6.81

2.50

2.80E−04

0.167774

 HP:0000219

Thin upper lip vermilion

137

26

12.78

2.03

2.84E−04

0.167774

 HP:0011228

Horizontal eyebrow

8

5

0.75

6.70

3.04E−04

0.167774

 HP:0005306

Capillary hemangioma

26

9

2.43

3.71

3.59E−04

0.167774

 HP:0001894

Thrombocytosis

21

8

1.96

4.08

3.63E−04

0.167774

 HP:0100559

Lower limb asymmetry

21

8

1.96

4.08

3.63E−04

0.167774

 HP:0000107

Renal cyst

203

34

18.93

1.80

4.21E−04

0.167774

  1. C reference genes in the category, O observed number of genes in the category, E expected number of genes in the category, R ratio of enrichment, pValue p value from hypergeometric test, FDR false discovery rate