Table 1.
Significantly enriched gene sets for genes downregulated following CBX2 depletion using siCBX2#3 in MDA-MB-231 cells. The 10 most significantly enriched gene sets from the Hallmark, Gene Ontology, and Oncogenic signature curated gene set database are shown. Gene sets are inversely ranked by normalised enrichment score (NES). SIZE = number of differentially expressed genes enriched in the gene set. NOM p-val = nominal p-value, FDR q-val = false discover rate q-value.
| Hallmark Gene Set | ||||
| NAME | SIZE | NES | NOM p-val | FDR q-val |
| HALLMARK_G2M_CHECKPOINT | 49 | −4.395 | <0.001 | <0.001 |
| HALLMARK_E2F_TARGETS | 45 | −4.221 | <0.001 | <0.001 |
| HALLMARK_XENOBIOTIC_METABOLISM | 48 | −2.373 | <0.001 | 0.005 |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 48 | −2.173 | 0.004 | 0.018 |
| HALLMARK_APOPTOSIS | 46 | −2.106 | 0.006 | 0.023 |
| HALLMARK_MITOTIC_SPINDLE | 46 | −1.989 | 0.006 | 0.037 |
| HALLMARK_MTORC1_SIGNALING | 45 | −1.902 | 0.012 | 0.050 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 56 | −1.866 | 0.010 | 0.054 |
| HALLMARK_UV_RESPONSE_UP | 33 | −1.864 | 0.008 | 0.048 |
| HALLMARK_MYC_TARGETS_V1 | 19 | −1.853 | 0.010 | 0.046 |
| Gene Ontology Gene Set | ||||
| NAME | SIZE | NES | NOM p-val | FDR q-val |
| GO_NEUROGENESIS | 288 | −3.522 | <0.001 | <0.001 |
| GO_CHROMOSOME_ORGANIZATION | 184 | −3.492 | <0.001 | <0.001 |
| GO_POSITIVE_REGULATION_OF_RESPONSE_TO_STIMULUS | 390 | −3.478 | <0.001 | <0.001 |
| GO_CELL_CYCLE | 233 | −3.416 | <0.001 | <0.001 |
| GO_REGULATION_OF_CELL_PROLIFERATION | 336 | −3.369 | <0.001 | <0.001 |
| GO_POSITIVE_REGULATION_OF_GENE_EXPRESSION | 347 | −3.362 | <0.001 | <0.001 |
| GO_CELL_PROLIFERATION | 134 | −3.360 | <0.001 | <0.001 |
| GO_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS | 168 | −3.295 | <0.001 | <0.001 |
| GO_POSITIVE_REGULATION_OF_CELL_PROLIFERATION | 185 | −3.286 | <0.001 | <0.001 |
| GO_CELL_DIVISION | 96 | −3.240 | <0.001 | <0.001 |
| Oncogenic Signature Gene Set | ||||
| NAME | SIZE | NES | NOM p-val | FDR q-val |
| RPS14_DN.V1_DN | 32 | −3.631 | <0.001 | <0.001 |
| E2F3_UP.V1_UP | 45 | −3.291 | <0.001 | <0.001 |
| PRC2_EZH2_UP.V1_DN | 46 | −2.782 | <0.001 | 0.002 |
| LEF1_UP.V1_UP | 47 | −2.593 | <0.001 | 0.005 |
| CSR_LATE_UP.V1_UP | 47 | −2.565 | <0.001 | 0.005 |
| NFE2L2.V2 | 87 | −2.331 | <0.001 | 0.015 |
| HOXA9_DN.V1_DN | 43 | −2.244 | <0.001 | 0.024 |
| BMI1_DN.V1_DN | 37 | −2.179 | 0.004 | 0.031 |
| CORDENONSI_YAP_CONSERVED_SIGNATURE | 20 | −2.140 | 0.002 | 0.035 |
| KRAS.600_UP.V1_DN | 53 | −2.099 | 0.004 | 0.040 |