Table 2.
The enrichment analysis result of NetGen on ulcerative colitis dataset
| 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 | ||
aGO:0032850 updated to alternate term GO:0043547
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