Table 1.
Number of terms included in the 65 statistically significant pathways found by pathfindR, divided by their involvement in a particular process and/or function and/organ
| Process/Function/Organ | Number of terms | top 5 upregulated genes |
top 5 downregulated genes |
||||
|---|---|---|---|---|---|---|---|
| gene | frequency | percent | gene | frequency | percent | ||
| Infection | 27 | TNFRSF1A | 14 | 51.9 | NFKBIA | 20 | 74.1 |
| FADD | 13 | 48.1 | PIK3R1 | 17 | 63.0 | ||
| HLA-A | 8 | 29.6 | AKT3 | 16 | 59.3 | ||
| HLA-B | 8 | 29.6 | JUN | 15 | 55.6 | ||
| HLA-C | 8 | 29.6 | CXCL8 | 14 | 51.9 | ||
| Cancer | 27 | GADD45G | 12 | 42.9 | AKT3 | 24 | 85.7 |
| PTEN | 12 | 42.9 | PIK3R1 | 24 | 85.7 | ||
| TGFA | 8 | 30.0 | JUN | 12 | 42.9 | ||
| BCL2L1 | 7 | 25.0 | FOS | 9 | 32.1 | ||
| WNT6 | 5 | 17.9 | NFKBIA | 8 | 28.6 | ||
| Metabolism | 23 | CREB3L3 | 7 | 30.4 | AKT3 | 19 | 82.6 |
| CREB5 | 7 | 30.4 | PIK3R1 | 16 | 69.6 | ||
| TNFRSF1A | 7 | 30.4 | PLCB1 | 11 | 47.8 | ||
| RXRA | 6 | 26.1 | PLCB4 | 11 | 47.8 | ||
| MMP9 | 5 | 21.7 | FOS | 8 | 34.8 | ||
| PTEN | 5 | 21.7 | |||||
| Immunology | 18 | HLA-A | 5 | 27.8 | NFKBIA | 9 | 50.0 |
| HLA-B | 5 | 27.8 | PIK3R1 | 9 | 50.0 | ||
| HLA-C | 5 | 27.8 | JUN | 8 | 44.4 | ||
| CCL5 | 4 | 22.2 | AKT3 | 6 | 33.3 | ||
| FADD | 4 | 22.2 | FOS | 6 | 33.3 | ||
| IFNGR2 | 4 | 22.2 | |||||
| PYCARD | 4 | 22.2 | |||||
| Neurodegeneration | 17 | BCL2L1 | 7 | 41.2 | AKT3 | 9 | 52.9 |
| TNFRSF1A | 6 | 35.3 | PIK3R1 | 9 | 52.9 | ||
| KLC3 | 5 | 29.4 | JUN | 7 | 41.2 | ||
| MAP2K3 | 5 | 29.4 | NDUFV2 | 6 | 35.3 | ||
| TUBB2A | 5 | 29.4 | FOS | 5 | 29.4 | ||
| TUBB4A | 5 | 29.4 | |||||
| Inflammation | 14 | CXCL1 | 3 | 21.4 | PIK3R1 | 6 | 42.9 |
| NCF1 | 3 | 21.4 | NFKBIA | 5 | 35.7 | ||
| ACTN1 | 2 | 14.3 | AKT3 | 4 | 28.6 | ||
| CCL5 | 2 | 14.3 | CXCL8 | 4 | 28.6 | ||
| CXCL6 | 2 | 14.3 | PLCB1 | 4 | 28.6 | ||
| FADD | 2 | 14.3 | PLCB4 | 4 | 28.6 | ||
| Cellular processes | 9 | ACTN1 | 4 | 44.4 | AKT3 | 4 | 44.4 |
| VASP | 3 | 33.3 | PIK3R1 | 4 | 44.4 | ||
| WAS | 3 | 33.3 | DOCK1 | 3 | 33.3 | ||
| FCGR2A | 2 | 22.2 | EEA1 | 2 | 22.2 | ||
| FCGR3B | 2 | 22.2 | FN1 | 2 | 22.2 | ||
| Neurotransmission | 6 | CAMK2A | 5 | 83.3 | AKT3 | 3 | 50.0 |
| CAMK2B | 5 | 83.3 | FOS | 3 | 50.0 | ||
| CREB3L3 | 3 | 50.0 | PIK3R1 | 3 | 50.0 | ||
| CREB5 | 3 | 50.0 | PLCB1 | 3 | 50.0 | ||
| CACNA1A | 2 | 33.3 | PLCB4 | 3 | 50.0 | ||
| Blood | 5 | IFNGR2 | 3.0 | 60.0 | AKT3 | 4.0 | 80.0 |
| IL6R | 3.0 | 60.0 | PIK3R1 | 4.0 | 80.0 | ||
| CSF1 | 2.0 | 40.0 | TFRC | 2.0 | 40.0 | ||
| CSF3R | 2.0 | 40.0 | CNTF | 1.0 | 20.0 | ||
| EPOR | 2.0 | 40.0 | FLT3 | 1.0 | 20.0 | ||
| Hormonal | 2 | ||||||
| Pregnancy | 1 | ||||||
| Heart | 1 | ||||||
| Circadian | 1 | ||||||
| Addiction | 1 | ||||||
The top five upregulated and downregulated genes among all terms included in each category are also indicated.