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Table 2 Significantly enriched pathways based on differential methylation in newborns exposed to maternal smoking during pregnancy

From: Maternal smoking impacts key biological pathways in newborns through epigenetic modification in Utero

Pathway Name

MSigDB Contributora

MSigDB Category Code

# Genes Pathway

# Genes Overlap

Discovery p value

Bonferroni Adjusted Discovery p value

Replication p value

Replication q value

Bonferroni Adjusted Replication p value

GSE17974_0H_VS_12H_IN_VITRO_ACT_CD4_TCELL_UP

Nick Haining lab (DFCI)

C7

200

172

1.56E-14

9.12E-11

9.31E-07

2.60E-05

4.28E-05

GSE17974_CTRL_VS_ACT_IL4_AND_ANTI_IL12_2H_CD4_TCELL_UP

Nick Haining lab (DFCI)

C7

200

171

3.01E-14

1.76E-10

1.13E-06

2.60E-05

5.19E-05

GSE17974_0H_VS_6H_IN_VITRO_ACT_CD4_TCELL_UP

Nick Haining lab (DFCI)

C7

200

169

1.55E-17

9.07E-14

5.33E-06

8.17E-05

0.0002

G1_S_TRANSITION_OF_MITOTIC_CELL_CYCLE

GO

C5

27

27

1.16E-18

6.74E-15

0.0012

0.0135

0.0548

WILLIAMS_ESR1_TARGETS_DN

Broad Institute

C2

6

6

1.83E-08

0.000107

0.0015

0.0135

0.0675

TIEN_INTESTINE_PROBIOTICS_2HR_UP

Broad Institute

C2

27

26

2.54E-08

0.000148

0.0019

0.0144

0.0862

TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP

Broad Institute

C2

21

21

6.48E-09

3.78E-05

0.0027

0.0158

0.1226

INTERPHASE_OF_MITOTIC_CELL_CYCLE

GO

C5

62

59

1.17E-16

6.85E-13

0.0027

0.0158

0.1264

HEDENFALK_BREAST_CANCER_BRACX_UP

University of Washington

C2

20

14

4.81E-10

2.80E-06

0.0032

0.0159

0.1464

ABE_VEGFA_TARGETS_2HR

University of Washington

C2

34

30

2.16E-09

1.26E-05

0.0036

0.0159

0.1675

INTERPHASE

GO

C5

68

65

7.20E-17

4.20E-13

0.0038

0.0159

0.1753

FRASOR_RESPONSE_TO_ESTRADIOL_UP

Broad Institute

C2

37

37

3.72E-08

0.000217

0.0046

0.0175

0.2099

ENGELMANN_CANCER_PROGENITORS_UP

Broad Institute

C2

48

47

4.18E-07

0.002441

0.0059

0.0209

0.2713

MIKKELSEN_IPS_WITH_HCP_H3K27ME3

Broad Institute

C2

102

97

4.80E-13

2.80E-09

0.0073

0.0239

0.3346

FALVELLA_SMOKERS_WITH_LUNG_CANCER

Broad Institute

C2

80

71

5.90E-08

0.000344

0.0091

0.0278

0.4165

AMUNDSON_GENOTOXIC_SIGNATURE

Broad Institute

C2

105

94

1.22E-15

7.15E-12

0.0110

0.0305

0.5045

GSE1460_DP_VS_CD4_THYMOCYTE_UP

Nick Haining lab (DFCI)

C7

200

174

1.29E-16

7.53E-13

0.0113

0.0305

0.5186

GSE3982_DC_VS_TH1_DN

Nick Haining lab (DFCI)

C7

200

174

4.75E-18

2.77E-14

0.0124

0.0307

0.5702

ELVIDGE_HIF1A_TARGETS_DN

Broad Institute

C2

91

85

2.82E-08

0.000165

0.0127

0.0307

0.5824

CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP

Broad Institute

C2

177

150

9.14E-14

5.34E-10

0.0140

0.0322

0.6444

GSE1460_DP_THYMOCYTE_VS_NAIVE_CD4_TCELL_ADULT_BLOOD_UP

Nick Haining lab (DFCI)

C7

200

170

3.93E-19

2.29E-15

0.0164

0.0353

0.7547

GSE17974_CTRL_VS_ACT_IL4_AND_ANTI_IL12_2H_CD4_TCELL_DN

Nick Haining lab (DFCI)

C7

200

181

1.27E-16

7.42E-13

0.0172

0.0353

0.7901

GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH2_DN

Nick Haining lab (DFCI)

C7

200

183

1.11E-15

6.48E-12

0.0194

0.0353

0.8933

GSE24634_NAIVE_CD4_TCELL_VS_DAY10_IL4_CONV_TREG_DN

Nick Haining lab (DFCI)

C7

200

185

5.91E-15

3.45E-11

0.0195

0.0353

0.8948

GSE3982_CENT_MEMORY_CD4_TCELL_VS_TH1_DN

Nick Haining lab (DFCI)

C7

200

185

1.44E-14

8.38E-11

0.0195

0.0353

0.8973

GSE17974_0H_VS_4H_IN_VITRO_ACT_CD4_TCELL_DN

Nick Haining lab (DFCI)

C7

200

182

1.43E-14

8.32E-11

0.0205

0.0353

0.9451

GSE3982_EOSINOPHIL_VS_TH1_DN

Nick Haining lab (DFCI)

C7

200

189

7.96E-15

4.65E-11

0.0209

0.0353

0.9599

GSE3982_NEUTROPHIL_VS_TH1_DN

Nick Haining lab (DFCI)

C7

200

182

2.96E-16

1.73E-12

0.0215

0.0353

0.9897

GSE24634_NAIVE_CD4_TCELL_VS_DAY7_IL4_CONV_TREG_DN

Nick Haining lab (DFCI)

C7

200

189

1.20E-15

7.00E-12

0.0250

0.0388

1

GSE15215_CD2_POS_VS_NEG_PDC_DN

Nick Haining lab (DFCI)

C7

200

180

3.26E-17

1.90E-13

0.0253

0.0388

1

GSE10856_CTRL_VS_TNFRSF6B_IN_MACROPHAGE_DN

Nick Haining lab (DFCI)

C7

200

170

1.47E-06

0.008573

0.0274

0.0407

1

GSE3982_MAC_VS_TH2_DN

Nick Haining lab (DFCI)

C7

200

182

5.98E-08

0.000349

0.0296

0.0426

1

  1. a Contributor to the corresponding pathway in MSigDB. Additional information about these contributors can be found at: http://www.broadinstitute.org/gsea/msigdb/collection_details.jsp
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