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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