Table 4.
The enrichment analysis result of NetGen on renal cell carcinoma dataset
| Rank | GO ID | Description | p-value |
|---|---|---|---|
| 1 | GO:0090259 | regulation of retinal ganglion cell axon guidance | 7.56e-7 |
| 2 | GO:0033572 | transferrin transport | 1.05e-6 |
| 3 | GO:0072017 | distal tubule development | 3.03e-5 |
| 4 | GO:2000054 | negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification | 3.34e-5 |
| 5 | GO:0072015 | glomerular visceral epithelial cell development | 1.17e-3 |
| 6 | GO:2000287 | positive regulation of myotome development | 5.81e-3 |
| 7 | GO:0006113 | fermentation | 5.81e-3 |
| 8 | GO:0051460 | negative regulation of corticotropin secretion | 5.81e-3 |
| 9 | GO:0060720 | spongiotrophoblast cell proliferation | 5.81e-3 |
| 10 | GO:0043438 | acetoacetic acid metabolic process | 5.81e-3 |
| 11 | GO:0032972 | regulation of muscle filament sliding speed | 5.81e-3 |
| 12 | GO:0090038 | negative regulation of protein kinase C signaling | 1.16e-2 |
| 13 | GO:0035425 | autocrine signaling | 1.16e-2 |
| 14 | GO:0010760 | negative regulation of macrophage chemotaxis | 1.16e-2 |
| 15 | GO:0060161 | positive regulation of dopamine receptor signaling pathway | 1.73e-2 |
| 16 | GO:0097411 | hypoxia-inducible factor-1alpha signaling pathway | 1.73e-2 |
| 17 | GO:0060435 | bronchiole development | 1.73e-2 |
| 18 | GO:0051933 | amino acid neurotransmitter reuptake | 1.73e-2 |
| 19 | GO:0046598 | positive regulation of viral entry into host cell | 2.31e-2 |
| 20 | GO:0015015 | heparan sulfate proteoglycan biosynthetic process, enzymatic modification | 2.87e-2 |
| 21 | GO:0006572 | tyrosine catabolic process | 2.87e-2 |
| 22 | GO:0019532 | oxalate transport | 2.87e-2 |
| 23 | GO:0072171 | mesonephric tubule morphogenesis | 3.44e-2 |
| 24 | GO:0051156 | glucose 6-phosphate metabolic process | 5.12e-2 |
| 25 | GO:0002542 | Factor XII activation | 1 |
| 26 | GO:0010766 | negative regulation of sodium ion transport | 1 |
| 27 | GO:0014858 | positive regulation of skeletal muscle cell proliferation | 1 |
Best parameter setting: p 1=0.5, p 2=0.05, q=0.001. Term combination p=8.68e-50
An appropriate parameter combination identified via a mixed parameter selection strategy was shown at the bottom of the table. The Fisher’s exact test p-values for single term and term combination were listed. The GO terms in bold were particularly identified by NetGen