TABLE 4.

PATHWAY ANALYSIS OF GENES DIFFERENTIALLY EXPRESSED IN LARGE AIRWAY EPITHELIAL CELLS GROWN AT AIR–LIQUID INTERFACE VERSUS LARGE AIRWAY BRUSHED CELLS*

Pathways with Genes with Increased Expression in Air–Liquid Interface Cells Relative to Brushed Cells			Pathways with Genes with Increased Expression in Brushed Cells Relative to Air–Liquid Interface Cells
Functional Pathway	Ratio†	P Value‡	Functional Pathway	Ratio†	P Value‡
Integrin signaling	0.26	3.18 × 10−9	Metabolism of xenobiotics by cytochrome p450	0.09	5.53 × 10−7
Ephrin receptor signaling	0.24	5.05 × 10−8	Fatty acid metabolism	0.08	2.57 × 10−4
IL-8 signaling	0.24	1.85 × 10−7	PXR/RXR activation	0.11	5.85 × 10−3
p53 signaling	0.32	6.02 × 10−7	Complement system	0.14	2.91 × 10−2
Cell cycle checkpoint regulation	0.31	3.53 × 10−5	Antigen presentation pathway	0.13	1.70 × 10−2

Definition of abbreviation: PXR/RXR, peroxisome proliferator activator receptor α/retinoid X receptor α.

^*Functional pathway analysis was carried out using Ingenuity Pathway Analysis (www.ingenuity.com) on all differentially expressed genes (magnitude of fold-change ALI cells compared to brushed cells > 2, P < 0.01, after Benjamini-Hochberg multiple test correction). Canonical pathways were selected on the basis of significance and ratio.

^†Ratio refers to the number of differentially expressed pathway genes compared to the total number of genes in the curated pathway.

^‡P value represents the likelihood that the association between the genes in the pathway is attributable to chance, calculated using the right-tailed Fisher exact test.