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Table 1 The enrichment analysis result of NetGen on lung cancer dataset

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

Rank GO ID Description p-value
1 GO:0006491 N-glycan processing 1.32e-3
2 GO:0006662 glycerol ether metabolic process 1.93e-3
3 GO:0006175 dATP biosynthetic process 5.54e-3
4 GO:0060149 negative regulation of posttranscriptional gene silencing 5.54e-3
5 GO:0006043 glucosamine catabolic process 5.54e-3
6 GO:0035772 interleukin-13-mediated signaling pathway 5.54e-3
7 GO:2000832 negative regulation of steroid hormone secretion 1.11e-2
8 GO:0021648 vestibulocochlear nerve morphogenesis 1.11e-2
9 GO:0072318 clathrin coat disassembly 1.11e-2
10 GO:1900748 positive regulation of vascular endothelial growth factor signaling pathway 1.65e-2
11 GO:0015014 heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process 1.65e-2
12 GO:0000710 meiotic mismatch repair 1.65e-2
13 GO:0030070 insulin processing 1.65e-2
14 GO:0072190 ureter urothelium development 1.65e-2
15 GO:0034154 toll-like receptor 7 signaling pathway 2.20e-2
16 GO:2000195 negative regulation of female gonad development 1
17 GO:0016082 synaptic vesicle priming 1
18 GO:2000370 positive regulation of clathrin-dependent endocytosis 1
19 GO:0002143 tRNA wobble position uridine thiolation 1
20 GO:0060978 angiogenesis involved in coronary vascular morphogenesis 1
  1. Best parameter setting: p 1=0.5, p 2=0.05, q=0.001. Term combination p=1.50e-24
  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