Table 3.
Pathway analysis of differentially expressed genes in cultured nasal epithelia vs. nasal brushings
| Pathway (Identifiers Found) | Ratio | P Value* |
|---|---|---|
| Pathways with genes with increased expression in NBR vs. CU | ||
| Formation of the cornified envelope (KRT13, SPRR3, SPRR2A, CSTA, SPRR2A) |
0.01 | 2.81E-10 |
| Keratinization (KRT13, SPRR3, SPRR2A, CSTA, SPRR1A) |
0.016 | 1.97E-08 |
| tRNA processing in the mitochondrion (MT-TP, MT-TL1, MT-TT, MT-TW, MT-TS1) |
0.003 | 2.57E-07 |
| Nuclear receptor transcription pathway (NR3C2) |
0.006 | 1.30E-04 |
| tRNA processing (MT-TP, MT-TL1, MT-TT, MT-TW, MT-TS1) |
0.013 | 2.06E-04 |
| rRNA processing in the mitochondrion (MT-TL1, MT-TT, MT-TW) |
0.003 | 2.42E-04 |
| Thyroxine biosynthesis (DU0X2) |
0.002 | 3.00E-03 |
| Developmental biology (KRT13, SPRR3, SPRR2A, CSTA, SPRR1A) |
0.084 | 8.23E-03 |
| MyD88 deficiency (TLR5, MYD88) | 0 | 8.90E-03 |
| Pathways with genes with decreased expression in NBR vs. CU | ||
| ECM organization (FBLN1, LAMC2, LAMA3, COL7A1, SERPINE1, LAMB3, ITGB4, TGFB2, ITGA3, ITGB6, ITGB6, ITGAV, TNC, FN1, LTBP2, COL1A1, CAPN13, COL17A1, SPARC, MMP13, HSPG2, THBS1, ICAM1) |
0.023 | 4.62E-11 |
| Type I hemidesmosome assembly (LAMC2, KRT17, LAMA3, KRT13, LAMB3, COL17A1, ITGB4) |
0.001 | 1.38E-8 |
| Laminin interactions (LAMC2, LAMA3, COL7A1, LAMB3, ITGB4, ITGA3, ITGAV, HSPG2) |
0.002 | 1.66E-8 |
| Non-integrin membrane-ECM interactions (LAMC2, KRT17, LAMA3, KRT13, LAMB3, COL17A1, ITGB4) |
0.004 | 1.88E-8 |
| FOXO-mediated transcription of cell cycle genes (TNC, FN1, LAMA3, SERPINE 1, COL1A1, SPARC, TGFB2, ITGB6, ITGAV, HSPG2) |
0.002 | 1.29E-8 |
| ECM proteoglycans (CDKN1A, CAV1, GADD45A) |
0.005 | 2.01E-7 |
| Integrin-cell surface interactions (TNC, FN1, COL7A1, COL1A1, ITGA3, ITGB6, ITGAV, HSPG2, THBS1, ICAM1) |
0.006 | 4.33E-7 |
| Assembly of collagen fibrils and other multimeric structures (TNC, LAMC2, LAMA3, COL7A1, LAMB3, COL1A1, COL17A1, ITGB4, MMP13) |
0.005 | 5.09E-7 |
| Anchoring fibril formation (LAMC2, LAMA3, COL7A1, LAMB4, COL1A1) |
0.001 | 2.53E-6 |
| MET promotes cell motility (FN1, LAMC2, LAMA3, LAMB3, COL1A1, TNS3, ITGA3) |
0.003 | 3.74E-6 |
| Syndecan interactions (TNC, FN1, COL1A1, ITGB4, ITGAV, THBS1) |
0.002 | 3.78E-6 |
| MET activates PTK2 signaling (FN1, LAMC2, LAMA3, LAMA3, LAMB3, COL1A1, ITGA3) |
0.002 | 6.59E-6 |
| Cell junction organization (FLNA, LAMC2, KRT17, LAMA3, KRT13, LAMB3, COL17A1, ITGB4, CDH3) |
0.007 | 7.8E-6 |
| Degradation of the ECM (TNC, FN1, LAMC2, LAMA3, COL7A1, LAMB3, COL1A1, CAPN13, COL17A1, MMP13, HSPG2) |
0.01 | 8.28E-6 |
| Collagen formation (TNC, LAMC2, LAMA3, COL7A1, LAMB3, COL1A1, COL17A1, ITGB4, MMP13) |
0.007 | 1.72E-5 |
| Molecules associated with elastic fibers (FN1, FBLN1, LTBP2, TGFB2, ITGB6, ITGAV) |
0.003 | 1.73E-5 |
| Cellular senescence (FLNA, CDKN1A, CDKN2A, IGFBP7, JUN, HES4) |
0.014 | 2.52E-5 |
| TP53 regulates transcription of cell cycle genes (PLK2, CDKN1A, GADD45A) |
0.005 | 3.9E-5 |
| IL-4 and IL-13 signaling (VIM, FN1, CDKN1A, SAA1, CCND1, ICAM1) |
0.015 | 4.41E-5 |
| Transcriptional regulation by RUNX3 (CDKN1A, CDKN2A, CTGF, CCND1) |
0.008 | 4.55E-5 |
Functional pathway analysis was carried out on differentially expressed genes from all 5 patients with chronic obstructive pulmonary disease. Ratio refers to percentage of total genes in the pathway. CU, cultured epithelia; ECM, extracellular matrix; MET, mesenchymal-epithelial transition factor; NBR, nasal brushing; PTK2, protein tyrosine kinase 2; RUNX3, runt-related transcription factor 3.
*
P ≤ 0.01 after Benjamini-Hochberg multiple test correction.