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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