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Table 5 Top 10 enriched gene setsa by alcohol consumptionb in tumor-adjacent normal samples in the NHS and the NHSII

From: Alcohol consumption and breast tumor gene expression

Pathway-defined gene set

Number of enriched genes

NES

FDR

ER+ tumor-adjacent normal tissues

 Upregulated

  KEGG_OLFACTORY_TRANSDUCTION

153

1.97

0.04

 Downregulated

  REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT

123

−2.33

<0.001

  REACTOME_SIGNALING_BY_WNT

60

−2.33

<0.001

  REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

39

−2.30

<0.001

  REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE

15

−2.28

<0.001

  KEGG_FOCAL_ADHESION

186

−2.27

<0.001

  BIOCARTA_RHO_PATHWAY

30

−2.27

<0.001

  BIOCARTA_INTEGRIN_PATHWAY

36

−2.26

<0.001

  BIOCARTA_PYK2_PATHWAY

27

−2.26

<0.001

  KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION

51

−2.25

<0.001

  REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM

151

−2.24

1.55E-04

ER- tumor-adjacent normal

 Up-regulated

  REACTOME_METABOLISM_OF_MRNA

206

2.87

<0.001

  REACTOME_METABOLISM_OF_RNA

248

2.79

<0.001

  REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX

106

2.66

<0.001

  REACTOME_INFLUENZA_LIFE_CYCLE

134

2.65

<0.001

  REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION

104

2.64

<0.001

  REACTOME_TRANSLATION

144

2.63

<0.001

  REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE

108

2.62

<0.001

  REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM

51

2.61

<0.001

  REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA

132

2.60

<0.001

  REACTOME_MRNA_PROCESSING

151

2.59

<0.001

 Down-regulated

   

  KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION

192

−2.52

<0.001

  REACTOME_GPCR_LIGAND_BINDING

297

−2.49

<0.001

  REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS

76

−2.36

<0.001

  REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS

212

−2.29

4.14E-04

  REACTOME_POTASSIUM_CHANNELS

86

−2.30

5.18E-04

  REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE

37

−2.20

2.04E-03

  GENERATION_OF_A_SIGNAL_INVOLVED_IN_CELL_CELL_SIGNALING

27

−2.14

3.22E-03

  REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS

36

−2.14

3.29E-03

  G_PROTEIN_SIGNALING_COUPLED_TO_CYCLIC_NUCLEOTIDE_SECOND_MESSENGER

83

−2.12

3.50E-03

  REACTOME_G_ALPHA_I_SIGNALLING_EVENTS

147

−2.12

3.50E-03

  1. ER estrogen receptor, NHS Nurses’ Health Study, NES normalized enrichment score, FDR false discovery rate
  2. aTop 10 ranked gene sets at FDR <0.05 are shown for upregulation and downregulation, respectively
  3. bEnriched gene sets for comparison of recent alcohol consumption 10+ vs. 0 g/day
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Breast Cancer Research

ISSN: 1465-542X

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