Table 3.
GSEA tests for enrichment of MSigDB C2 gene sets
| Gene Set Name | Size | ES | NES | NOM p-value | FDR q-value | ||
|---|---|---|---|---|---|---|---|
| Acute exposure | Down-regulated | None | |||||
| Up-regulated | XU_CBP_UP | 19 | 0.633 | 1.987 | 0.000 | 0.051 | |
| CALRES_MOUSE_DN | 28 | 0.575 | 1.920 | 0.000 | 0.108 | ||
| BYSTRYKH_HSC_CIS_GLOCUS | 82 | 0.516 | 1.889 | 0.000 | 0.097 | ||
| BYSTRYKH_HSC_BRAIN_CIS_GLOCUS | 43 | 0.600 | 1.855 | 0.000 | 0.102 | ||
| PENG_GLUTAMINE_DN | 209 | 0.519 | 1.828 | 0.000 | 0.130 | ||
| UVC_LOW_ALL_DN | 38 | 0.473 | 1.817 | 0.000 | 0.121 | ||
| CMV_ALL_UP | 64 | 0.530 | 1.764 | 0.000 | 0.214 | ||
| SANSOM_APC_LOSS5_UP | 55 | 0.544 | 1.734 | 0.037 | 0.274 | ||
| BLEO_MOUSE_LYMPH_HIGH_24HRS_DN | 31 | 0.669 | 1.730 | 0.000 | 0.255 | ||
| SHEPARD_CRASH_AND_BURN_MUT_VS_WT_UP | 124 | 0.452 | 1.710 | 0.000 | 0.289 | ||
| PENG_RAPAMYCIN_DN | 163 | 0.516 | 1.706 | 0.023 | 0.275 | ||
| PRMT5_KD_DN | 19 | 0.572 | 1.694 | 0.038 | 0.298 | ||
| HSA00970_AMINOACYL_TRNA_BIOSYNTHESIS | 29 | 0.702 | 1.690 | 0.029 | 0.286 | ||
| MRNA_SPLICING | 44 | 0.633 | 1.689 | 0.000 | 0.266 | ||
| WANG_MLL_CBP_VS_GMP_DN | 30 | 0.579 | 1.688 | 0.000 | 0.254 | ||
| JAIN_NEMO_DIFF | 59 | 0.458 | 1.688 | 0.000 | 0.240 | ||
| HSA00563_GLYCOSYLPHOSPHATIDYLINOSITOL_ANCHOR_BIOSYNTHESIS | 16 | 0.616 | 1.684 | 0.000 | 0.239 | ||
| BLEO_MOUSE_LYMPH_LOW_24HRS_DN | 22 | 0.697 | 1.681 | 0.000 | 0.238 | ||
| OLDONLY_FIBRO_UP | 28 | 0.485 | 1.674 | 0.000 | 0.243 | ||
| CMV_24HRS_UP | 54 | 0.524 | 1.673 | 0.000 | 0.232 | ||
| KUROKAWA_5FU_IFN_SENSITIVE_VS_RESISTANT_DN | 22 | 0.624 | 1.669 | 0.000 | 0.232 | ||
| CHANG_SERUM_RESPONSE_UP | 109 | 0.480 | 1.668 | 0.000 | 0.224 | ||
| ROS_MOUSE_AORTA_UP | 21 | 0.731 | 1.656 | 0.036 | 0.237 | ||
| UVB_NHEK2_DN | 64 | 0.456 | 1.649 | 0.000 | 0.242 | ||
| SCHUMACHER_MYC_UP | 44 | 0.504 | 1.649 | 0.023 | 0.234 | ||
| STEMCELL_COMMON_UP | 149 | 0.458 | 1.643 | 0.023 | 0.242 | ||
| MYC_ONCOGENIC_SIGNATURE | 137 | 0.406 | 1.641 | 0.000 | 0.239 | ||
| ZHAN_MMPC_SIM_BC_AND_MM | 36 | 0.472 | 1.635 | 0.000 | 0.242 | ||
| AMINOACYL_TRNA_BIOSYNTHESIS | 21 | 0.732 | 1.633 | 0.048 | 0.238 | ||
| Chronic exposure | Down-regulated | TNFR1PATHWAY | 24 | -0.724 | -1.968 | 0.000 | 0.026 |
| CASPASEPATHWAY | 16 | -0.684 | -1.865 | 0.000 | 0.049 | ||
| DEATHPATHWAY | 25 | -0.719 | -1.836 | 0.000 | 0.063 | ||
| HIVNEFPATHWAY | 44 | -0.593 | -1.765 | 0.000 | 0.104 | ||
| MITOCHONDRIAPATHWAY | 17 | -0.785 | -1.728 | 0.000 | 0.151 | ||
| TSA_PANC50_UP | 25 | -0.584 | -1.684 | 0.000 | 0.216 | ||
| Up-regulated | None |
Results for MSigDB C2 gene sets (drawn from 1892 sets representing all systems, pathways and functions in that database), listing sets with NES scores that are both statistically significant and below the FDR threshold. Size refers to the number of genes in the set; ES and NES are the enrichment scores and normalized enrichment scores (respectively) for the set; NOM p-value is the nominal p-value for the NES, FDR q-vlaue is the false discovery rate ratio (values lower than 0.25 are considered to be passing as per Subramanian et al. [4]). One of these sets (in bold) is a liver associated set highlighted in Table 4.