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Table 4 The enrichment analysis result of NetGen on renal cell carcinoma dataset

From: NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis

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
  1. Best parameter setting: p 1=0.5, p 2=0.05, q=0.001. Term combination p=8.68e-50
  2. 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