Improving the power of gene set enrichment analyses

Roder, Joanna; Linstid, Benjamin; Oliveira, Carlos

doi:10.1186/s12859-019-2850-1

BMC Bioinformatics

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

From: Improving the power of gene set enrichment analyses

Gene Set	p value with ES	p value with ES_avg	p value with <ES_avg>
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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