Table 2.
Top 20 significant GO (biological process) terms associated with transcripts that were differentially expressed between the treated and untreated groups
| GO_ID | Term | Annotated | Significant | Expected | p-value |
|---|---|---|---|---|---|
| GO:0006355 | Regulation of transcription, DNA-template | 2829 | 129 | 110 | 3.3e-26 |
| GO:0051301 | Cell division | 510 | 96 | 19.83 | 5.0e-26 |
| GO:0006281 | DNA repair | 358 | 47 | 13.92 | 4.6e-25 |
| GO:0007067 | Mitotic nuclear division | 309 | 74 | 13.92 | 2.1e-23 |
| GO:0006397 | mRNA processing | 317 | 23 | 12.33 | 4.2e-23 |
| GO:0007049 | Cell cycle | 1129 | 167 | 43.9 | 1.2e-19 |
| GO:0008380 | RNA splicing | 254 | 17 | 9.88 | 5.5e-19 |
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | 539 | 41 | 20.96 | 6.6e-19 |
| GO:0015031 | Protein transport | 1256 | 63 | 48.84 | 9.5e-19 |
| GO:0006886 | Intracellular protein transport | 651 | 38 | 25.31 | 2.6e-18 |
| GO:0006364 | rRNA processing | 111 | 3 | 4.32 | 4.2e-15 |
| GO:0016567 | Protein ubiquitination | 484 | 28 | 18.82 | 1.7e-14 |
| GO:0045944 | Positive regulation of transcription from RNA polymerase II promoter | 716 | 45 | 27.84 | 4.5e-14 |
| GO:0006260 | DNA replication | 232 | 51 | 9.02 | 1.1e-13 |
| GO:0045893 | Positive regulation of transcription, DNA template | 1074 | 62 | 41.76 | 4.7e-13 |
| GO:0045892 | Negative regulation of transcription, DNA template | 860 | 58 | 33.44 | 1.8e-11 |
| GO:0001701 | In utero embryonic development | 371 | 29 | 14.43 | 2.9e-11 |
| GO:0006915 | Apoptotic process | 1336 | 91 | 51.95 | 6.5e-11 |
| GO:0051726 | Regulation of cell cycle | 560 | 82 | 21.77 | 1.2e-10 |
| GO:0008285 | Negative regulation of cell proliferation | 449 | 30 | 17.46 | 2.4e-10 |
This table aims to highlight the most relevant GO terms associated with the differentially expressed transcripts in the comparison to ascertain whether certain biological functions were enriched among the transcripts compared with the reference background. This analysis is a type of gene enrichment test and does not ensure that the transcripts that belong to a significant GO term are up or downregulated. It does ensure, however, that a group of differentially expressed genes with similar functionality are significantly over-represented. The expected values represent an estimate of the number of transcripts associated with the given significant GO term at random among all the annotated differentially expressed genes. The significant (observed) values represent the number of differentially expressed transcripts associated with that particular GO term in the sample (real) dataset. Annotations represent the total number of genes associated with that GO term in the sample dataset, which means that the reference background could potentially have a larger number of annotations. The q value represents the test statistics for the given GO term whether or not it is significantly enriched