Table 3. Pathways significantly enriched among the DEGs and DEEs between good and poor prognosis groups.
| Pathway name | Input/total no. of genes | FDR |
|---|---|---|
| Gene level | ||
| Antigen processing and presentation | 2/89 | <0.001 |
| Circadian rhythm | 2/13 | <0.001 |
| JAK/STAT signaling pathway | 7/155 | 0.001 |
| Hematopoietic cell lineage | 5/87 | 0.003 |
| Biosynthesis of unsaturated fatty acids | 3/22 | 0.004 |
| Exon level (top 20 pathways) | ||
| Antigen processing and presentation | 17/89 | <0.001 |
| Leukocyte transendothelial migration | 22/119 | <0.001 |
| Cell adhesion molecules (CAMs) | 26/134 | <0.001 |
| Adherens junction | 19/78 | <0.001 |
| Phosphatidylinositol signaling system | 21/76 | <0.001 |
| ECM receptor interaction | 33/84 | <0.001 |
| Focal adhesion | 59/203 | <0.001 |
| Pathways in cancer | 84/330 | <0.001 |
| Calcium signaling pathway | 50/182 | <0.001 |
| ABC transporters | 19/44 | <0.001 |
| MAPK signaling pathway | 64/272 | <0.001 |
| Long-term depression | 25/75 | <0.001 |
| Tight junction | 36/135 | <0.001 |
| Amyotrophic lateral sclerosis (ALS) | 19/56 | 0.001 |
| Small cell lung cancer | 25/86 | 0.001 |
| VEGF signaling pathway | 22/74 | 0.002 |
| Axon guidance | 33/129 | 0.002 |
| Type I diabetes mellitus | 14/44 | 0.002 |
| Regulation of actin cytoskeleton | 47/217 | 0.003 |
| Thyroid cancer | 11/29 | 0.003 |
Abbreviations: ABC, adenosine triphosphate-binding cassette; ECM, extracellular matrix; DEE, differentially expressed exon; DEG, differentially expressed gene; FDR, false discovery rate; JAK/STAT, Janus kinase/signal transducer and activator of transcription; MAPK, mitogen-activated protein kinase; VEGF, vascular endothelial growth factor.