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Table 1 p values for the 50 Hallmarks gene sets. p values were calculated using the 294 sample cohort using ES, ESavg or < ESavg > with 25 splits as the test statistic. Gene sets are sorted by increasing p value obtained using ESavg as the statistic

From: Improving the power of gene set enrichment analyses

Gene Set p value with ES p value with ESavg p value with <ESavg>
MTORC1_SIGNALING < 0.0001 < 0.0001 < 0.0001
E2F_TARGETS < 0.0001 < 0.0001 < 0.0001
UV_RESPONSE_UP 0.0132 < 0.0001 < 0.0001
G2M_CHECKPOINT < 0.0001 < 0.0001 < 0.0001
PI3K_AKT_MTOR_SIGNALING 0.0040 0.0002 < 0.0001
MITOTIC_SPINDLE 0.0028 0.0004 < 0.0001
UNFOLDED_PROTEIN_RESPONSE 0.0006 0.0004 < 0.0001
REACTIVE_OXIGEN_SPECIES_PATHWAY 0.0063 0.0004 0.0002
ESTROGEN_RESPONSE_EARLY 0.0068 0.0006 0.0002
SPERMATOGENESIS 0.0185 0.0006 0.0002
GLYCOLYSIS 0.0216 0.0012 0.0008
MYC_TARGETS_V1 0.0172 0.0020 0.0002
UV_RESPONSE_DN 0.0156 0.0020 0.0012
MYC_TARGETS_V2 0.0320 0.0032 0.0026
DNA_REPAIR 0.0263 0.0035 0.0008
INTERFERON_GAMMA_RESPONSE 0.0373 0.0046 0.0038
IL6_JAK_STAT3_SIGNALING 0.0790 0.0074 0.0081
INTERFERON_ALPHA_RESPONSE 0.0638 0.0080 0.0105
COMPLEMENT 0.1059 0.0157 0.0149
ESTROGEN_RESPONSE_LATE 0.0622 0.0188 0.0080
ALLOGRAFT_REJECTION 0.0684 0.0194 0.0144
INFLAMMATORY_RESPONSE 0.0963 0.0303 0.0172
CHOLESTEROL_HOMEOSTASIS 0.1035 0.0449 0.0252
BILE_ACID_METABOLISM 0.0966 0.0472 0.0247
ANGIOGENESIS 0.2591 0.0796 0.0753
WNT_BETA_CATENIN_SIGNALING 0.4422 0.1160 0.1235
EPITHELIAL_MESENCHYMAL_TRANSITION 0.2984 0.1219 0.0984
COAGULATION 0.2516 0.1223 0.1093
IL2_STAT5_SIGNALING 0.1685 0.1437 0.0596
MYOGENESIS 0.2767 0.1589 0.1043
TGF_BETA_SIGNALING 0.3229 0.1593 0.1344
OXIDATIVE_PHOSPHORYLATION 0.3773 0.1877 0.1604
PROTEIN_SECRETION 0.3107 0.2032 0.2028
ADIPOGENESIS 0.4204 0.2247 0.2581
APICAL_SURFACE 0.4078 0.2477 0.0824
P53_PATHWAY 0.5724 0.2489 0.2423
TNFA_SIGNALING_VIA_NFKB 0.3401 0.2509 0.1545
HYPOXIA 0.4398 0.2712 0.2450
APOPTOSIS 0.5796 0.2905 0.3886
APICAL_JUNCTION 0.5175 0.2907 0.2579
NOTCH_SIGNALING 0.7451 0.3104 0.3226
FATTY_ACID_METABOLISM 0.5358 0.3134 0.3853
PANCREAS_BETA_CELLS 0.6834 0.3201 0.1500
XENOBIOTIC_METABOLISM 0.4921 0.3541 0.4946
HEME_METABOLISM 0.7713 0.4576 0.4731
KRAS_SIGNALING_UP 0.6241 0.7068 0.4892
ANDROGEN_RESPONSE 0.8082 0.7539 0.5841
HEDGEHOG_SIGNALING 0.7870 0.7810 0.5163
PEROXISOME 0.3931 0.8977 0.3682
KRAS_SIGNALING_DN 0.9700 0.9193 0.7337
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BMC Bioinformatics

ISSN: 1471-2105

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