Table 2.
Top gene set significantly enriched in untreated compared to MMC (n=9) treated by DNMTi/HDACi combination
| Gene set name | Genes in gene set (K) | Description | Genes in overlap (k) | k/K | P-value | FDR q-value |
|---|---|---|---|---|---|---|
| HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP | 461 | Genes upregulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562] | 49 | 0.1063 | 8.57E-31 | 4.06E-27 |
| SENESE_HDAC3_TARGETS_DN | 536 | Genes downregulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi | 41 | 0.0765 | 1.58E-20 | 1.07E-17 |
| PILON_KLF1_TARGETS_DN | 1972 | Genes downregulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild-type embryos | 78 | 0.0396 | 7.34E-20 | 4.35E-17 |
| HELLER_SILENCED_BY_METHYLATION_DN | 105 | Genes downregulated in at least one of the three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668] | 20 | 0.1905 | 2.33E-18 | 1.03E-15 |
| HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN | 281 | Genes downregulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562] | 29 | 0.1032 | 2.39E-18 | 1.03E-15 |
| MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 | 1069 | Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation at K4 (H3K4me2) and trimethylation at K27 (H3K27me3) in the brain | 52 | 0.0486 | 4.33E-17 | 1.47E-14 |
| HELLER_HDAC_TARGETS_UP | 317 | Genes upregulated in at least one of the three multiple myeloma (MM) cell lines by TSA [PubChem=5562] | 29 | 0.0915 | 6.26E-17 | 1.98E-14 |
| NUYTTEN_EZH2_TARGETS_UP | 1037 | Genes upregulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi | 49 | 0.0473 | 1.13E-15 | 2.97E-13 |
| NUYTTEN_EZH2_TARGETS_DN | 1024 | Genes downregulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi | 46 | 0.0449 | 5.41E-14 | 1.03E-11 |
| HELLER_SILENCED_BY_METHYLATION_UP | 282 | Genes upregulated in at least one of the three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668] | 24 | 0.0851 | 1.50E-13 | 2.49E-11 |
| CHICAS_RB1_TARGETS_CONFLUENT | 567 | Genes upregulated in confluent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi | 33 | 0.0582 | 2.26E-13 | 3.45E-11 |
| HELLER_HDAC_TARGETS_DN | 292 | Genes downregulated in at least one of the three multiple myeloma (MM) cell lines by TSA [PubChem=5562] | 24 | 0.0822 | 3.20E-13 | 4.74E-11 |
| DANG_BOUND_BY_MYC | 1103 | Genes whose promoters are bound by MYC [GeneID=4609], according to MYC Target Gene Database | 46 | 0.0417 | 7.35E-13 | 9.56E-11 |
| ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP | 66 | Genes upregulated in CD-1 compared to CD-2 cluster of multiple myeloma samples | 13 | 0.197 | 1.32E-12 | 1.53E-10 |
| WEI_MYCN_TARGETS_WITH_E_BOX | 795 | Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [GeneID=4613] | 37 | 0.0465 | 6.23E-12 | 6.71E-10 |
| MARTINEZ_TP53_TARGETS_DN | 593 | Genes downregulated in mice with skin-specific knockout of TP53 [GeneID=7157] | 31 | 0.0523 | 1.89E-11 | 1.79E-09 |
| MARTINEZ_RB1_TARGETS_UP | 673 | Genes upregulated in mice with skin-specific knockout of RB1 [GeneID=5925] by Cre-lox | 32 | 0.0475 | 1.00E-10 | 7.29E-09 |
| PUJANA_ATM_PCC_NETWORK | 1442 | Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC≥0.4) with that of ATM [GeneID=472] across a compendium of normal tissues | 49 | 0.034 | 1.75E-10 | 1.23E-08 |
| SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE | 101 | IRF4 [GeneID=3662] target genes up-regulated in primary myeloma vs. mature B lymphocytes | 13 | 0.1287 | 3.57E-10 | 2.32E-08 |
| MARTINEZ_RB1_AND_TP53_TARGETS_DN | 591 | Genes downregulated in mice with skin-specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox | 29 | 0.0491 | 3.71E-10 | 2.37E-08 |
| SENESE_HDAC1_TARGETS_UP | 457 | Genes upregulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi | 25 | 0.0547 | 6.79E-10 | 3.92E-08 |
| BILD_MYC_ONCOGENIC_SIGNATURE | 206 | Genes selected in supervised analyses to discriminate cells expressing c-Myc [GeneID=4609] from control cells expressing GFP | 17 | 0.0825 | 8.63E-10 | 4.92E-08 |
| CHICAS_RB1_TARGETS_GROWING | 243 | Genes upregulated in growing IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi | 18 | 0.0741 | 1.57E-09 | 8.46E-08 |
| BENPORATH_CYCLING_GENES | 648 | Genes showing cell-cycle stage-specific expression [PMID=12058064] | 29 | 0.0448 | 2.99E-09 | 1.48E-07 |
| REACTOME_CELL_CYCLE | 421 | Genes involved in cell cycle | 23 | 0.0546 | 3.36E-09 | 1.61E-07 |
| CHICAS_RB1_TARGETS_SENESCENT | 572 | Genes upregulated in senescent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi | 27 | 0.0472 | 3.44E-09 | 1.63E-07 |