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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