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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