Table 3. Gene set enrichment analysis for differentially expressed genes in low grade and high grade phenotype of case 2.
| Gene Set Name | # Genes in Gene Set (K) | # Genes in Overlap (k) | k/K | Enrichment score (ES) | p-value | FDR q-value | |
|---|---|---|---|---|---|---|---|
| A. Gene sets enriched with genes over-expressed in high grade phenotype | |||||||
| (a) | MILI_PSEUDOPODIA_HAPTOTAXIS_DN | 668 | 41 | 0.0614 | 0.2736 | 8.04E-22 | 3.80E-18 |
| (b) | GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN | 1080 | 50 | 0.0463 | 0.1704 | 4.58E-21 | 1.08E-17 |
| (c) | PATIL_LIVER_CANCER | 747 | 31 | 0.0415 | 0.2521 | 3.19E-12 | 1.07E-9 |
| (d) | MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 | 1069 | 47 | 0.0440 | 0.2492 | 5.88E-19 | 9.25-16 |
| (e) | VERHAAK_GLIOBLASTOMA_PRONEURAL | 210 | 21 | 0.1000 | 0.3899 | 6.36E-16 | 6.00E-13 |
| (f) | REACTOME_BETA_DEFENSINS | 42 | 11 | 0.2619 | 0.8475 | 9.75E-14 | 5.76E-11 |
| (g) | BENPORATH_SUZ12_TARGETS | 1038 | 43 | 0.0414 | 0.2278 | 1.70e-16 | 2.01E-13 |
| B. Gene sets enriched with genes underexpressed in high grade phenotype | |||||||
| (a) | BLALOCK_ALZHEIMERS_DISEASE_UP | 1691 | 48 | 0.0284 | −0.2388 | 3.69E-12 | 1.16E-9 |
| (b) | LU_AGING_BRAIN_UP | 262 | 17 | 0.0649 | −0.3781 | 3.77E-10 | 8.09E-8 |