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Table 2 The enrichment analysis result of NetGen on ulcerative colitis dataset

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

Rank

GO ID

Description

p-value

1

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

1.10e-3

2

GO:0018874

benzoate metabolic process

3.83e-3

3

GO:0010900

negative regulation of phosphatidylcholine catabolic process

3.83e-3

4

GO:1900402

regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter

3.83e-3

5

GO:0006294

nucleotide-excision repair, preincision complex assembly

3.83e-3

6

GO:0038193

thromboxane A2 signaling pathway

3.83e-3

7

GO:0031119

tRNA pseudouridine synthesis

7.65e-3

8

GO:0007439

ectodermal digestive tract development

7.65e-3

9

GO:0009240

isopentenyl diphosphate biosynthetic process

1.15e-2

10

GO:0045196

establishment or maintenance of neuroblast polarity

1.15e-2

11

GO:0006154

adenosine catabolic process

1.15e-2

12

GO:0002254

kinin cascade

1.15e-2

13

GO:2000681

negative regulation of rubidium ion transport

1.15e-2

14

GO:0035701

hematopoietic stem cell migration

1.52e-2

15

GO:0008612

peptidyl-lysine modification to peptidyl-hypusine

1.52e-2

16

GO:1901299

negative regulation of hydrogen peroxide-mediated programmed cell death

1

17

GO:1901841

regulation of high voltage-gated calcium channel activity

1

18

GO:0043547 a

positive regulation of GTPase activity

1

Best parameter setting: p 1=0.5, p 2=0.05, q=0.001.

Term combination p=1.33e-27

 
  1. aGO:0032850 updated to alternate term GO:0043547
  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