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