Skip to main content

Table 4 Enriched gene setsa by recent alcohol consumptionb in ER- tumors in the NHS and the NHSII

From: Alcohol consumption and breast tumor gene expression

Pathway-defined gene set Number of enriched genes NES FDR
Upregulated
 REACTOME_TRANSLATION 144 2.31 0.0002
 REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM 218 2.32 0.0003
 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS 124 2.38 0.001
 REACTOME_METABOLISM_OF_MRNA 206 2.25 0.001
 PROTEIN_RNA_COMPLEX_ASSEMBLY 60 2.25 0.001
 REACTOME_INTERFERON_SIGNALING 129 2.21 0.001
 REACTOME_METABOLISM_OF_RNA 248 2.18 0.001
 REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 108 2.17 0.001
 REACTOME_INFLUENZA_LIFE_CYCLE 134 2.13 0.002
 KEGG_SPLICEOSOME 122 2.10 0.002
 KEGG_RIBOSOME 84 2.08 0.003
 BIOCARTA_CDC42RAC_PATHWAY 15 2.08 0.003
 REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION 104 2.07 0.003
 REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX 106 2.05 0.003
 REACTOME_PEPTIDE_CHAIN_ELONGATION 85 2.03 0.004
 REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES 61 2.01 0.005
 RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY 79 1.97 0.006
 REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA 132 1.97 0.006
 REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION 101 1.94 0.008
 REACTOME_MRNA_PROCESSING 151 1.92 0.009
 RNA_PROCESSING 159 1.88 0.013
 BIOCARTA_G1_PATHWAY 25 1.84 0.017
 RNA_SPLICING 87 1.82 0.020
 REACTOME_MRNA_SPLICING 104 1.80 0.023
 REACTOME_CELL_CYCLE 328 1.79 0.024
 REACTOME_CELL_CYCLE_CHECKPOINTS 97 1.78 0.026
 CELLULAR_COMPONENT_ASSEMBLY 272 1.75 0.030
 REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER 271 1.75 0.030
 MRNA_METABOLIC_PROCESS 78 1.74 0.031
 REACTOME_HIV_INFECTION 183 1.74 0.031
 RANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER 427 1.73 0.032
 REACTOME_SIGNALING_BY_BMP 21 1.72 0.032
 REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER 33 1.72 0.033
 REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S 56 1.71 0.034
 REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX 56 1.70 0.037
 REACTOME_CELL_CYCLE_MITOTIC 255 1.70 0.037
 NUCLEAR_EXPORT 31 1.68 0.041
 REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY 18 1.68 0.041
 POSITIVE_REGULATION_OF_NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS 143 1.68 0.042
 KEGG_RNA_DEGRADATION 55 1.67 0.042
 KEGG_ADHERENS_JUNCTION 70 1.67 0.043
 G1_S_TRANSITION_OF_MITOTIC_CELL_CYCLE 25 1.67 0.045
 REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM 51 1.66 0.045
 POSITIVE_REGULATION_OF_TRANSCRIPTION 134 1.65 0.048
Downregulated
 None    
  1. ER estrogen receptor, NHS Nurses’ Health Study, NES normalized enrichment score, FDR false discovery rate
  2. aOnly gene sets replicated in The Cancer Genome Atlas (TCGA) dataset and FDR <0.05 are shown
  3. bEnriched gene sets for comparison of recent alcohol consumption 10+ vs. 0 g/day