Table 1. GSEA of genes which expression depends on high FACT level.
| Functional group | Gene Set Name | # Genes in Gene Set |
Description | # Genes in Overlap (k) | k/K | p-value | FDR q- value |
|---|---|---|---|---|---|---|---|
| DNA replication, proliferation, cell cycle | CHANG_CYCLING_GENES | 148 | Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. | 49 | 0.3311 | 2.04E-88 | 2.40E-85 |
| BENPORATH_CYCLING_ GENES | 648 | Genes showing cell-cycle stage-specific expression [PMID=12058064]. |
60 | 0.0926 | 7.85E-73 | 5.30E-70 | |
| REACTOME_CELL_CYCLE_ MITOTIC |
325 | Genes involved in Cell Cycle, Mitotic | 40 | 0.1231 | 1.07E-52 | 1.73E-50 | |
| BENPORATH_ PROLIFERATION | 147 | Set 'Proliferation Cluster': genes defined in human breast tumor expression data. | 32 | 0.2177 | 1.46E-50 | 2.09E-48 | |
| REACTOME_CELL_CYCLE | 421 | Genes involved in Cell Cycle | 41 | 0.0974 | 1.01E-49 | 1.25E-47 | |
| WHITFIELD_CELL_CYCLE_ LITERATURE | 44 | A list of known cell cycle regulated genes that was compiled from the literature by the authors. | 21 | 0.4773 | 6.68E-42 | 6.18E-40 | |
| REACTOME_MITOTIC_G1_ G1_S_PHASES | 137 | Genes involved in Mitotic G1-G1/S phases | 18 | 0.1314 | 1.95E-24 | 9.68E-23 | |
| WHITFIELD_CELL_CYCLE_ G2 | 182 | Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2 phase of cell cycle. | 19 | 0.1044 | 9.03E-24 | 4.35E-22 | |
| REACTOME_ DNA_REPLICATION | 192 | Genes involved in DNA Replication | 24 | 0.125 | 9.16E-32 | 5.93E-30 | |
| E2F targets | MARSON_BOUND_BY_ E2F4_UNSTIMULATED | 728 | Genes with promoters bound by E2F4 [GeneID=1874] in unstimulated hybridoma cells. | 56 | 0.0769 | 5.03E-63 | 1.32E-60 |
| KONG_E2F3_TARGETS | 97 | Genes up-regulated in MEF cells (embryonic fibroblasts) at 16 hr after serum stimulation and knockdown of E2F3 [GeneID=1871] by RNAi. | 23 | 0.2371 | 2.23E-37 | 1.78E-35 | |
| ISHIDA_E2F_TARGETS | 53 | Genes up-regulated in MEF cells (embryonic fibroblast) after expression of E2F1 or E2F2 [GeneID=1869;1870]. |
18 | 0.3396 | 1.11E-32 | 7.48E-31 | |
| Undifferentiated cell state | BENPORATH_ES_1 | 379 | Set 'ES exp1′: genes overexpressed in human embryonic stem cells according to 5 or more out of 20 profiling studies. | 34 | 0.0897 | 7.51E-40 | 6.57E-38 |
| SARRIO_EPITHELIAL_ MESENCHYMAL_ TRANSITION_UP | 180 | Genes up-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. | 34 | 0.1889 | 1.97E-51 | 3.10E-49 | |
| WONG_EMBRYONIC_ STEM_CELL_CORE | 335 | The 'core ESC-like gene module': genes coordinately up- regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module. | 31 | 0.0925 | 9.57E-37 | 7.53E-35 | |
| RHODES_UNDIFFERENTIA TED_CANCER | 69 | Genes commonly up-regulated in undifferentiated cancer relative to well-differentiated cancer, based on the meta-analysis of the OncoMine gene expression database. | 20 | 0.2899 | 1.36E-34 | 1.02E-32 | |
| Upregulated in response to oncogenes | 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]. | 35 | 0.044 | 2.91E-30 | 1.81E-28 |
| YU_MYC_TARGETS_UP | 42 | Genes up-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. | 15 | 0.3571 | 8.57E-28 | 5.12E-26 | |
| OXFORD_RALA_OR_RALB _TARGETS_UP |
48 | Genes up-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. | 14 | 0.2917 | 1.49E-24 | 7.48E-23 | |
| KOBAYASHI_EGFR_ SIGNALING_24HR_DN | 251 | Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. | 71 | 0.2829 | 5.70E-125 | 2.69E-121 | |
| BERENJENO_ TRANSFORMED_ BY_RHOA_UP | 536 | Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. | 54 | 0.1007 | 4.18E-67 | 1.64E-64 |