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Table 2 Top pathways identified in comparisons between current (C), former (F), and never (N) smokers. Pathways identified as differentially expressed with p < 0.05 using pathway activity levels in comparisons between smokers and non-smokers. The p-values were determined using 10,000 random permutations as described in the Methods section. p < 0.0001 means no pathway in any of the 10,000 permutations showed higher significance. We note that the change (up or down) is determined, somewhat arbitrarily, by the average expression level captured by the first metagene. Specifically, the pathway is called 'up' if the average of ∑ i c j w i is greater in the first group (e.g., C in 'C vs. N') than in the second. A given pathway, however, will typically have some genes with higher and some with lower mean expression in one group as compared to another.

From: Pathway level analysis of gene expression using singular value decomposition

Comparison (genes in data set/total genes in pathway) Pathway p change
C vs. N (14/45) gamma-Hexachlorocyclohexane degradation <0.0001 down
  (15/39) Prostaglandin and leukotriene metabolism <0.0001 up
  (11/24) O-Glycans biosynthesis <0.0001 up
  (6/21) Pentose and glucuronate interconversions <0.0001 up
  (24/34) Glutathione metabolism <0.0001 up
  (3/12) Lectin Induced Complement Pathway 0.0004 down
  (11/19) Chaperones modulate interferon Signaling Pathway 0.0006 up
  (6/15) TACI and BCMA stimulation of B cell immune responses. 0.0044 down
  (3/6) Tetrachloroethene degradation 0.0054 up
  (3/6) FXR and LXR Regulation of Cholesterol Metabolism 0.0062 down
  (4/7) TSP-1 Induced Apoptosis in Microvascular Endothelial Cell 0.0065 down
  (16/28) Galactose metabolism 0.0067 down
  (13/20) Biosynthesis of steroids 0.0164 up
  (7/11) Map Kinase Inactivation of SMRT Corepressor 0.0274 down
  (25/68) Nicotinate and nicotinamide metabolism 0.0279 up
  (4/14) Classical Complement Pathway 0.0314 down
  (6/19) Complement Pathway 0.0364 down
  (9/13) Nucleotide sugars metabolism 0.0369 up
  (3/3) Degradation of the RAR and RXR by the proteasome 0.0396 down
F vs. C (3/12) Lectin Induced Complement Pathway 0.0068 up
  (13/20) Biosynthesis of steroids 0.0083 down
  (24/34) Glutathione metabolism 0.0403 down
F vs. N (14/45) gamma-Hexachlorocyclohexane degradation 0.0321 down