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. 2020 Apr 1;318(5):L1056–L1062. doi: 10.1152/ajplung.00050.2020

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.