Table 3 Running the GOSS-FEAT for specific GO Ids and using different GO term semantic similarity approaches
From: DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures
Approach | GO-ID | GO name | Level | Reference fuzzy | Target fuzzy | p-value | Corrected |
|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | Frequency | Frequency | Â | p-value |
GO-Universal | GO:0051409 | Response to nitrosative stress | 3 | 91 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0006979 | Response to oxidative stress | 3 | 90 | 18 | 8.08e-13 | 5.17e-11 |
| Â | GO:0052572 | Response to host immune response | 7 | 92 | 8 | 1.16e-07 | 7.45e-06 |
Wang et al. | GO:0006979 | Response to oxidative stress | 3 | 226 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0046677 | Response to antibiotic | 4 | 164 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0001666 | Response to hypoxia | 5 | 163 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0006974 | Response to DNA damage stimulus | 5 | 419 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0009432 | SOS response | 5 | 316 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0034605 | Cellular response to heat | 5 | 351 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0071500 | Cellular response to nitrosative stress | 5 | 365 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0075136 | Response to host | 5 | 293 | 12 | 9.10e-08 | 5.82e-06 |
Resnik | GO:0009432 | SOS response | 5 | 294 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0034605 | Cellular response to heat | 5 | 296 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0071500 | Cellular response to nitrosative stress | 5 | 294 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0009267 | Cellular response to starvation | 6 | 294 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0071456 | Cellular response to hypoxia | 7 | 370 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0071732 | Cellular response to nitric oxide | 7 | 369 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0006284 | Base-excision repair | 8 | 361 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0006289 | Nucleotide-excision repair | 8 | 361 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0006307 | DNA dealkylation involved in DNA repair | 9 | 424 | 18 | 0.00e+00 | 0.00e+00 |
| Â | GO:0052059 | Evasion or tolerance by symbiont of host- | 11 | 319 | 18 | 1.63e-12 | 1.04e-10 |
| Â | Â | produced reactive oxygen species | Â | Â | Â | Â | Â |
| Â | GO:0052060 | Evasion or tolerance by symbiont of host- | 11 | 319 | 18 | 1.63e-12 | 1.04e-10 |
| Â | Â | produced nitric oxide | Â | Â | Â | Â | Â |
| Â | GO:0051701 | Interaction with host | 4 | 35 | 6 | 1.05e-07 | 6.74e-06 |