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Table 3 The enrichment analysis result of NetGen on cervical carcinogenesis dataset

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

Rank

GO ID

Description

p-value

1

GO:0006271

DNA strand elongation involved in DNA replication

3.42e-11

2

GO:0090224

regulation of spindle organization

1.78e-3

3

GO:0001927

exocyst assembly

6.43e-3

4

GO:0038016

insulin receptor internalization

6.43e-3

5

GO:0070676

intralumenal vesicle formation

6.43e-3

6

GO:0086042

cardiac muscle cell-cardiac muscle cell adhesion

6.43e-3

7

GO:0014738

regulation of muscle hyperplasia

1.28e-2

8

GO:2000393

negative regulation of lamellipodium morphogenesis

1.28e-2

9

GO:0010993

regulation of ubiquitin homeostasis

1.28e-2

10

GO:0006050

mannosamine metabolic process

1.28e-2

11

GO:0046602

regulation of mitotic centrosome separation

1.92e-2

12

GO:0072708

response to sorbitol

1.92e-2

13

GO:0001992

regulation of systemic arterial blood pressure by vasopressin

1.92e-2

14

GO:1902498

regulation of protein autoubiquitination

1.92e-2

15

GO:0048388

endosomal lumen acidification

1.92e-2

16

GO:0048280

vesicle fusion with Golgi apparatus

2.55e-2

17

GO:0097264

self proteolysis

3.18e-2

18

GO:0045329

carnitine biosynthetic process

3.18e-2

19

GO:0051382

kinetochore assembly

7.45e-2

20

GO:0000741

karyogamy

1

21

GO:2000656

regulation of apolipoprotein binding

1

22

GO:0032848

negative regulation of cellular pH reduction

1

23

GO:0090158

endoplasmic reticulum membrane organization

1

  1. Best parameter setting: p 1=0.5, p 2=0.05, q=0.001. Term combination p=1.10e-37
  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