Table 2 Hypergeometric test comparing the percentage of differentially express genes between clusters that belong to the following specific signatures. Statistically significant results are highlighted in bold
From: Lung immune signatures define two groups of end-stage IPF patients
Cluster 1 | Cluster 2 | |||||
|---|---|---|---|---|---|---|
OR | Matched genes (%) | p-value | OR | Matched genes (%) | p-value | |
Immune signatures | ||||||
Activated T cells | 59.30 | 50.00 | 1.62E−03 | 0 | 0 | 1 |
Activated B cells | 37.55 | 38.46 | 1.43E−06 | 0 | 0 | 1 |
Activated CD4 | 0 | 0 | 1 | 0 | 0 | 1 |
Activated CD8 | 0 | 0 | 1 | 0 | 0 | 1 |
Central memory CD4 | 8.48 | 12.50 | 0.03 | 0 | 0 | 1 |
Central memory CD8 | 40.20 | 40.00 | 8.92E−08 | 0 | 0 | 1 |
Cytotoxic cells | 59.78 | 50.00 | 5.00E−06 | 0 | 0 | 1 |
Effector memory CD4 | 0 | 0 | 1 | 1.85 | 8.33 | 0.44 |
Effector memory CD8 | 22.88 | 27.27 | 2.34E−09 | 0 | 0 | 1 |
Immature B cells | 32.60 | 35.00 | 2.12E−08 | 0 | 0 | 1 |
Memory B cells | 13.20 | 18.18 | 0.01 | 0 | 0 | 1 |
NK cells | 4.55 | 7.14 | 0.21 | 0 | 0 | 1 |
NK CD56 bright | 0 | 0 | 1 | 0 | 0 | 1 |
NK CD56 dim | 0 | 0 | 1 | 0 | 0 | 1 |
NKT cells | 9.86 | 14.29 | 0.11 | 0 | 0 | 1 |
T follicular helper | 23.75 | 28.57 | 5.50E−03 | 0 | 0 | 1 |
TGD | 5.76 | 8.82 | 0.02 | 0 | 0 | 1 |
Th1 | 38.30 | 38.46 | 5.82E−12 | 0 | 0 | 1 |
Th17 | 0 | 0 | 1 | 1.07 | 5.00 | 0.62 |
Th2 | 11 | 15 | 0 | 0.00 | 0.00 | 1.00 |
Viral response | 24.15 | 28.20 | 2.46E−11 | 0 | 0 | 1 |
Epithelial signatures | ||||||
EMT | 0 | 0 | 1 | 4.79 | 18.87 | 1.49E−04 |
Epithelial | 0 | 0 | 1 | 12.65 | 38.10 | 2.63E−06 |
Basal cells | 3.43 | 5.45 | 0.06 | 2.99 | 12.73 | 0.01 |
Activated basals | 5.38 | 8.33 | 0.18 | 1.85 | 8.33 | 0.44 |
Aberrant basaloid | 0 | 0 | 1 | 0 | 0 | 1 |
Primed basals | 6.58 | 10.00 | 0.15 | 8.75 | 30.00 | 0.01 |
Proliferative basals | 0 | 0 | 1.00 | 0 | 0 | 1 |
Multipotent basal | 3.29 | 5.26 | 0.27 | 3.83 | 15.79 | 0.06 |
Secretory cells | 0 | 0 | 1 | 15.82 | 43.33 | 2.68E−10 |
Club cells | 0 | 0 | 1 | 40.89 | 66.67 | 6.64E−05 |
Globet cells | 0 | 0 | 1 | 51.53 | 71.43 | 4.03E−11 |
Mucous cells | 0 | 0 | 1 | 16.85 | 45.00 | 1.09E−07 |
Serous cells | 0 | 0 | 1 | 7.98 | 28.00 | 1.10E−04 |
MUC5Bpos | 0 | 0 | 1 | 143.70 | 87.50 | 3.69E−09 |
Cilliated cells | 0 | 0 | 1 | 4.26 | 17.24 | 0.01 |
Cilliated cells type 1 | 0 | 0 | 1 | 82.57 | 80.00 | 4.07E−14 |
Cilliated cells type 2 | 0 | 0 | 1 | 102.45 | 83.33 | 1.28E−06 |
Differentiated cilliated | 0 | 0 | 1 | 309.85 | 93.75 | 1.52E−19 |
IPF cilium associated signatures [11] | ||||||
Pattern A | 0 | 0 | 1 | 2139.52 | 98.92 | 1.23E−123 |
Pattern B | 1.00 | 1.67 | 0.64 | 54.66 | 71.67 | 3.64E−44 |
Fibrosis associated signatures | ||||||
Fibrosis | 0 | 0 | 1 | 0 | 0 | 1 |
Fibroblast activation | 0 | 0 | 1 | 0 | 0 | 1 |
Lipofibroblast | 0 | 0 | 1 | 0 | 0 | 1 |
Myofibroblast | 0 | 0 | 1 | 0 | 0 | 1 |
Smooth muscle cells | 0 | 0 | 1 | 0 | 0 | 1 |
Myofibroblast | 0 | 0 | 1 | 0 | 0 | 1 |
Pericytes | 0 | 0 | 1 | 0 | 0 | 1 |
Extracellular matrix | 1.2 | 2.12 | 0.36 | 0.47 | 3.72 | 0.99 |
Matrix features | 0 | 0 | 1 | 0 | 0 | 1 |
Response to pirfenidone | 0 | 0 | 1 | 1.27 | 5.88 | 0.56 |
TGFb signaling | 4.23 | 7.14 | 0.22 | 0 | 0 | 1 |
Senescence | 0 | 0 | 1 | 0.48 | 2.33 | 0.87 |
G0 to early G1 | 0 | 0 | 1 | 1.20 | 5.56 | 0.58 |
G1 to S cycle | 0 | 0 | 1 | 0.57 | 2.76 | 0.91 |
G2 to M cycle | 0 | 0 | 1 | 0.49 | 2.37 | 0.96 |
Mitochondrial transport | 1.21 | 2.17 | 0.57 | 0.28 | 2.17 | 0.96 |
Mitochondrial respiratory chain | 0 | 0 | 1 | 0 | 0 | 1 |
Response to stress | 5.25 | 7.94 | 4.50E−08 | 0.43 | 3.34 | 0.99 |
Oxidative stress | 3.37 | 5.68 | 0.02 | 0.29 | 2.27 | 0.99 |
Pro-oxidant | 5.82 | 9.52 | 0.05 | 0 | 0 | 1 |
Oxidative response | 5.5 | 9.09 | 0.18 | 0 | 0 | 1 |
Antioxidant | 4.61 | 7.69 | 0.07 | 0 | 0 | 1 |