Table 3. Biological enrichment analysis for the top 10 hubs in the ssMIKANA, tsMIKANA and cMIKANA network models.
| ssMIKANA | ||||
| Gene Ontology | Genes with Annotation | ln(Bayes factor) | FE: -ln(p value) | FE: -ln(FDR) |
| GO:0006952: defense response | 8 | 13.02 | 15.55 | 11.01 |
| GO:0051244: regulation of cellular physiological process | 7 | 12.56 | 15.09 | 11.01 |
| GO:0009607: response to biotic stimulus | 8 | 11.99 | 14.51 | 10.84 |
| GO:0006955: immune response | 7 | 10.7 | 13.22 | 9.84 |
| GO:0050794: regulation of cellular process | 7 | 10.31 | 12.83 | 9.69 |
| GO:0051243: negative regulation of cellular physiological process | 5 | 10.13 | 12.67 | 9.69 |
| GO:0050791: regulation of physiological process | 10 | 9.43 | 11.95 | 9.12 |
| GO:0050789: regulation of biological process | 10 | 8.34 | 10.84 | 8.15 |
| GO:0006954: inflammatory response | 4 | 7.94 | 10.48 | 7.97 |
| GO:0043118: negative regulation of physiological process | 5 | 7.92 | 10.44 | 7.97 |
| GO:0006366: transcription from Pol II promoter | 5 | 7.79 | 10.31 | 7.94 |
| GO:0006916: anti-apoptosis | 3 | 6.82 | 9.37 | 7.08 |
| GO:0050896: response to stimulus | 8 | 6.67 | 9.16 | 7 |
| GO:0043066: negative regulation of apoptosis | 3 | 6.49 | 9.03 | 7 |
| GO:0009611: response to wounding | 4 | 6.48 | 9 | 7 |
| GO:0043069: negative regulation of programmed cell death | 3 | 6.46 | 9 | 7 |
| TransFac | ||||
| V$NFKAPPAB65_01: NF-kappaB (p65) | 7 | 9.66 | 12.19 | 6.69 |
| V$NFKB_C: NF-kappaB binding site | 5 | 6.88 | 9.39 | 4.59 |
The categories in Gene Ontology and TransFac with Bayes factor >6 are summarized and the related number of genes with annotation in the hubs. The Fisher exact p-value (FE: -ln[p value]) and false discovery rate (FE: -ln[FDR]) are presented.