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Table 3 GSEA tests for enrichment of MSigDB C2 gene sets

From: Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a non-mammalian model organism

   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      
  1. 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.