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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